Genes that were induced specifically by IFN-beta, but not the IFN-alpha subtypes tested
Association between genes and clinical outcomes
## check the counts of gene list
cnts.geneid <- rownames_to_column(data.frame(cnts.deseq2), var = "Gene_ID")
dim(cnts.geneid)
## [1] 19890 33
cnts.isgs <- base::merge(cnts.geneid, isgs, by = "Gene_ID") %>%
select(-c("Gene_ID")) %>% column_to_rownames(var = "Symbol")
dim(cnts.isgs)
## [1] 230 32
cnts.isgs <- as.matrix(cnts.isgs)
## QC plots
EDASeq::plotRLE(cnts.isgs, outline = FALSE, col = c(rep("steelblue",
13), rep("tomato", 19)), main = "Control vs. HIV RLE Plot (Core ISGs DESeq2 Normalization)",
xlab = "Sample", ylab = "Relative Log Ratio")

EDASeq::plotPCA(cnts.isgs, col = c(rep("steelblue", 13), rep("tomato",
19)), main = "Control vs. HIV PCA Plot (Core ISGs DESeq2 Normalization)")

EDASeq::plotPCA(cnts.isgs, col = c(rep("steelblue", 13), rep("tomato",
19)), main = "Control vs. HIV PCA Plot (Core ISGs DESeq2 Normalization)",
k = 3)

boxplot(log2(cnts.isgs), main = "Control vs. HIV Boxplot (Core ISGs DESeq2 Normalization)",
xlab = "Sample", ylab = "log2 Counts")

## beta specific genesbeta
cnts.genesbeta <- base::merge(cnts.geneid, genesbeta, by = "Gene_ID") %>%
select(-c("Gene_ID")) %>% column_to_rownames(var = "Symbol")
dim(cnts.genesbeta)
## [1] 423 32
cnts.genesbeta <- as.matrix(cnts.genesbeta)
## QC plots
EDASeq::plotRLE(cnts.genesbeta, outline = FALSE, col = c(rep("steelblue",
13), rep("tomato", 19)), main = "Control vs. HIV RLE Plot (IFN-beta Genes DESeq2 Normalization)",
xlab = "Sample", ylab = "Relative Log Ratio")

EDASeq::plotPCA(cnts.genesbeta, col = c(rep("steelblue", 13),
rep("tomato", 19)), main = "Control vs. HIV PCA Plot (IFN-beta Genes DESeq2 Normalization)")

EDASeq::plotPCA(cnts.genesbeta, col = c(rep("steelblue", 13),
rep("tomato", 19)), main = "Control vs. HIV PCA Plot (IFN-beta Genes DESeq2 Normalization)",
k = 3)

boxplot(log2(cnts.genesbeta), main = "Control vs. HIV Boxplot (IFN-beta Genes DESeq2 Normalization)",
xlab = "Sample", ylab = "log2 Counts")

# ## Voom transformation ## The voom method estimates the
# mean-variance relationship of the log-counts, ## generates
# a precision weight for each observation and enters these
# into the limma empirical Bayes analysis pipeline. ## two
# group design design <- model.matrix(~0 + pheno$txt) v <-
# voom(cnts.isgs, design, plot=TRUE) v voom is more suitable
# for edgeR
########################### VST Transformation ###################### DESeq2 has VST,
########################### yielding a matrix of values which are now approximately
########################### homoskedastic (having constant variance along the range of
########################### mean values). are useful when checking for outliers or as
########################### input for machine learning techniques such as clustering or
########################### linear discriminant analysis.
## check size factors
dds$sizeFactor
## C138 C178 C255 C278 C361 C404 C493
## 0.2801477 0.3829072 1.2625914 1.3744154 1.4832384 2.3577403 0.8480453
## C582 C708 C716 C914 C947 C972 H124
## 2.0025479 1.1997877 3.9008838 2.1250832 0.6948343 2.5525922 0.8290624
## H132 H154 H188 H217 H286 H307 H323
## 1.1309331 1.0691897 1.4909671 0.9222770 0.4492812 1.0551965 1.0524649
## H391 H428 H594 H622 H648 H683 H819
## 0.7188160 0.3511746 4.0518366 0.9162538 1.1020128 0.3013386 0.7619062
## H825 H839 H965 H998
## 0.5903655 0.7926637 0.2150957 6.0910728
paste("The size factors vary a lot.")
## [1] "The size factors vary a lot."
# ## vst transformation dds <-
# varianceStabilizingTransformation(dds, blind = FALSE,
# fitType = 'parametric') getVarianceStabilizedData(object)
# If many of genes have large differences in counts due to
# the experimental design, it is important to set blind=FALSE
# for downstream analysis. The more the size factors differ,
# the more residual dependence of the variance on the mean
# will be found in the transformed data. rlog is a
# transformation which can perform better in these cases.
rld <- rlog(dds, blind = FALSE, fitType = "parametric")
var.cnts.rld <- assay(rld)
## get linear model ready cnts for core isgs and beta specific
var.rld <- rownames_to_column(data.frame(var.cnts.rld))
colnames(var.rld)[1] <- c("Gene_ID")
## gene level dataset
var.isgs <- base::merge(var.rld, isgs.de, by = "Gene_ID") %>%
dplyr::mutate(Symbol = Symbol.x) %>% select(-c(Symbol.x,
Symbol.y))
dim(var.isgs)
## [1] 230 38
var.genesbeta <- base::merge(var.rld, genesbeta.de, by = "Gene_ID") %>%
dplyr::mutate(Symbol = Symbol.x) %>% select(-c(Symbol.x,
Symbol.y))
dim(var.genesbeta)
## [1] 423 38
## clustering core isgs
dist.isgs <- dist(t(var.isgs[, 2:33]))
plot(hclust(dist.isgs, method = "complete"), main = "Cluster Dendrogram by Core ISGs")

## beta specific
dist.genesbeta <- dist(t(var.genesbeta[, 2:33]))
plot(hclust(dist.genesbeta, method = "complete"), main = "Cluster Dendrogram by IFN-beta Genes")

## kmeans cluster
## kmeans and try k
maxk <- 7
k_c <- 1:maxk
k_sws <- NULL
k_wsm <- NULL
for (i in k_c) {
km <- kmeans(t(var.isgs[, 2:33]), i, iter.max = 10)
k_sws[i] <- sum(km$withinss)
if (i == 1) {
k_wsm <- c(km$withinss)
} else {
k_wsm <- c(k_wsm, km$withinss)
}
}
plot(k_c, k_sws, type = "o", xlab = "Number of Clusters by Core ISGs",
ylab = "Sum of Within cluster sum of squares")

## kmeans for isgs
kisgs6 <- kmeans(t(var.isgs[, 2:33]), 6, iter.max = 10)
kisgs6$cluster
## C138 C178 C255 C278 C361 C404 C493 C582 C708 C716 C914 C947 C972 H124 H132
## 5 6 5 5 6 5 5 5 5 6 5 5 5 1 1
## H154 H188 H217 H286 H307 H323 H391 H428 H594 H622 H648 H683 H819 H825 H839
## 1 2 1 1 3 2 1 3 2 2 4 4 3 6 3
## H965 H998
## 4 2
## beta
for (i in k_c) {
km <- kmeans(t(var.genesbeta[, 2:33]), i, iter.max = 10)
k_sws[i] <- sum(km$withinss)
if (i == 1) {
k_wsm <- c(km$withinss)
} else {
k_wsm <- c(k_wsm, km$withinss)
}
}
plot(k_c, k_sws, type = "o", xlab = "Number of Clusters by IFN-Beta Genes",
ylab = "Sum of Within cluster sum of squares")

## kmeans for beta
kgbeta3 <- kmeans(t(var.genesbeta[, 2:33]), 3, iter.max = 10)
kgbeta3$cluster
## C138 C178 C255 C278 C361 C404 C493 C582 C708 C716 C914 C947 C972 H124 H132
## 1 3 3 1 1 3 3 3 1 1 1 3 1 3 3
## H154 H188 H217 H286 H307 H323 H391 H428 H594 H622 H648 H683 H819 H825 H839
## 3 1 3 3 3 3 3 2 1 1 2 2 2 1 2
## H965 H998
## 2 1
################## linear regression ################ import age, gender and
################## clinical outcomes by pid basic clinical data
basic_cli_CH <- read.delim("Basic_clinical_control_infected_untreated")
colnames(basic_cli_CH) <- c("pid", "sex", "age", "CD4_Counts",
"Plasma_Viral_Load")
# check pid
rna.pid
## [1] "C138" "C178" "C255" "C278" "C361" "C404" "C493" "C582" "C708" "C716"
## [11] "C914" "C947" "C972" "H124" "H132" "H154" "H188" "H217" "H286" "H307"
## [21] "H323" "H391" "H428" "H594" "H622" "H648" "H683" "H819" "H825" "H839"
## [31] "H965" "H998"
basic_cli_CH$pid[basic_cli_CH$pid %nin% rna.pid]
## [1] "H319" "H196" "H868" "H339" "H456" "C119"
#### sample level dataset isgs
isgs.rld.raw <- as.matrix(t(var.isgs[, 2:33]))
colnames(isgs.rld.raw) <- var.isgs$Symbol
## row id to column pid
isgs.rld.raw <- data.frame(isgs.rld.raw)
isgs.rld.raw$pid <- rownames(isgs.rld.raw)
rownames(isgs.rld.raw) <- NULL
## combine gene counts and clinical data
isgs.rld.lin <- base::merge(isgs.rld.raw, basic_cli_CH, by = "pid")
dim(isgs.rld.lin)
## [1] 32 235
##### sample level dataset genesbeta
genesbeta.rld.raw <- as.matrix(t(var.genesbeta[, 2:33]))
colnames(genesbeta.rld.raw) <- var.genesbeta$Symbol
## row id to column pid
genesbeta.rld.raw <- data.frame(genesbeta.rld.raw)
genesbeta.rld.raw$pid <- rownames(genesbeta.rld.raw)
rownames(genesbeta.rld.raw) <- NULL
## combine gene counts and clinical data
genesbeta.rld.lin <- base::merge(genesbeta.rld.raw, basic_cli_CH,
by = "pid")
dim(genesbeta.rld.lin)
## [1] 32 428
## check same pid
sum(isgs.rld.lin$pid == genesbeta.rld.lin$pid)
## [1] 32
# the same order of pid
########################## linear regression ############################## equal
########################## length of outcomes and covariates
gene_FunReg <- function(gene_matrix, clinical_variable, genelistname,
clin_var_name) {
## number of gene to test, also the number of multiple test
n_gene = ncol(gene_matrix)
## outcome lm
outcome_lm = lapply(1:n_gene, function(i) {
lm = lm(gene_matrix[, i] ~ clinical_variable + isgs.rld.lin$age +
isgs.rld.lin$sex)
coef = summary(lm)$coefficients[2, ]
return(coef)
})
outcome_lm = data.frame(matrix(unlist(outcome_lm), ncol = 4,
byrow = TRUE, dimnames = list(c(colnames(gene_matrix)),
c("Estimate", "Std.Error", "t.statistic", "p.value"))))
# adjusted p-value
outcome_lm = outcome_lm %>% dplyr::mutate(FDR = p.adjust(p.value,
"BH", n_gene), names = colnames(gene_matrix)) %>% dplyr::mutate(Estimate = round(Estimate,
10), Std.Error = round(Std.Error, 10), t.statistic = round(t.statistic,
4)) %>% select(names, everything())
# sort by p.value
outcome_lm = outcome_lm[order(outcome_lm$p.value), ]
## sample size
size = length(clinical_variable) - sum(clinical_variable)
## summary table
kable(outcome_lm, caption = paste("Top Genes from ", genelistname,
" Associated with Outcome: ", clin_var_name, " by p.value",
" (Sample Size = ", size, ") ", sep = "", collapse = ""),
digits = c(2, 10, 10, 4, 20, 20))
}
############# viral load #################### after rlog the count data
############# to the log2 scale whole isgs
gene_FunReg(as.matrix(isgs.rld.lin[, 2:231]), isgs.rld.lin[,
235], "Core ISGs", "Plasma Viral Load")
Top Genes from Core ISGs Associated with Outcome: Plasma Viral Load by p.value (Sample Size = NA)
| 30 |
SMCHD1 |
-1.7840e-06 |
4.5940e-07 |
-3.8831 |
0.001471060 |
0.2136266 |
| 84 |
SNX6 |
-2.6289e-06 |
6.9750e-07 |
-3.7689 |
0.001857623 |
0.2136266 |
| 214 |
ASAH2B |
7.9078e-06 |
2.2198e-06 |
3.5624 |
0.002836082 |
0.2174330 |
| 210 |
CD2AP |
-2.3665e-06 |
7.3750e-07 |
-3.2086 |
0.005859761 |
0.3369363 |
| 99 |
TRAFD1 |
5.3036e-06 |
1.7176e-06 |
3.0879 |
0.007500727 |
0.3450334 |
| 165 |
TLR3 |
4.9896e-06 |
1.7056e-06 |
2.9254 |
0.010443083 |
0.4003182 |
| 32 |
FMR1 |
-2.3666e-06 |
8.5150e-07 |
-2.7794 |
0.014030289 |
0.4289824 |
| 178 |
SNTB1 |
4.6487e-06 |
1.6912e-06 |
2.7488 |
0.014921127 |
0.4289824 |
| 39 |
GIMAP2 |
5.5667e-06 |
2.3089e-06 |
2.4110 |
0.029192260 |
0.7460244 |
| 203 |
TDRD7 |
6.9213e-06 |
3.0309e-06 |
2.2836 |
0.037390883 |
0.7913862 |
| 52 |
TRIM38 |
-1.9743e-06 |
8.6700e-07 |
-2.2773 |
0.037848904 |
0.7913862 |
| 116 |
PARP9 |
6.7003e-06 |
3.0046e-06 |
2.2300 |
0.041449447 |
0.7925806 |
| 124 |
ZCCHC2 |
-2.3946e-06 |
1.0937e-06 |
-2.1893 |
0.044798033 |
0.7925806 |
| 143 |
SLC25A28 |
3.6153e-06 |
1.6889e-06 |
2.1407 |
0.049133916 |
0.8072000 |
| 213 |
RNY4P34 |
-3.3733e-06 |
1.8026e-06 |
-1.8714 |
0.080923296 |
0.9694104 |
| 180 |
AFF1 |
4.0322e-06 |
2.1918e-06 |
1.8396 |
0.085697477 |
0.9694104 |
| 137 |
IFIT5 |
3.6948e-06 |
2.0378e-06 |
1.8132 |
0.089864720 |
0.9694104 |
| 11 |
TBC1D1 |
-1.2962e-06 |
7.2910e-07 |
-1.7778 |
0.095713985 |
0.9694104 |
| 177 |
PRKCE |
-2.4329e-06 |
1.3723e-06 |
-1.7729 |
0.096552260 |
0.9694104 |
| 158 |
GPR155 |
-3.0475e-06 |
1.7681e-06 |
-1.7235 |
0.105335663 |
0.9694104 |
| 222 |
TRIM26 |
-3.1203e-06 |
1.8195e-06 |
-1.7150 |
0.106928741 |
0.9694104 |
| 53 |
CCND3 |
-2.6477e-06 |
1.5666e-06 |
-1.6901 |
0.111678367 |
0.9694104 |
| 181 |
MYD88 |
4.2295e-06 |
2.5028e-06 |
1.6900 |
0.111706778 |
0.9694104 |
| 126 |
MVB12A |
-3.1735e-06 |
1.8911e-06 |
-1.6781 |
0.114026753 |
0.9694104 |
| 110 |
CMTR1 |
1.5366e-06 |
9.4860e-07 |
1.6200 |
0.126064659 |
0.9694104 |
| 100 |
CD164 |
4.7499e-06 |
2.9417e-06 |
1.6147 |
0.127210627 |
0.9694104 |
| 18 |
CHMP5 |
5.4749e-06 |
3.4212e-06 |
1.6003 |
0.130377932 |
0.9694104 |
| 130 |
DYNLT1 |
5.7765e-06 |
3.6808e-06 |
1.5694 |
0.137412305 |
0.9694104 |
| 133 |
ENDOD1 |
-2.0503e-06 |
1.3317e-06 |
-1.5396 |
0.144474012 |
0.9694104 |
| 211 |
TMEM229B |
-3.4447e-06 |
2.2731e-06 |
-1.5154 |
0.150457288 |
0.9694104 |
| 106 |
RTP4 |
3.8892e-06 |
2.5955e-06 |
1.4985 |
0.154763127 |
0.9694104 |
| 7 |
TMSB10 |
3.2836e-06 |
2.2023e-06 |
1.4910 |
0.156697863 |
0.9694104 |
| 73 |
ODF2L |
1.2424e-06 |
8.4210e-07 |
1.4755 |
0.160764883 |
0.9694104 |
| 70 |
KIAA1217 |
-1.2459e-06 |
8.4820e-07 |
-1.4688 |
0.162532511 |
0.9694104 |
| 142 |
TTC39B |
-1.6511e-06 |
1.1313e-06 |
-1.4595 |
0.165044535 |
0.9694104 |
| 131 |
TMEM140 |
2.3106e-06 |
1.6644e-06 |
1.3883 |
0.185330593 |
0.9694104 |
| 164 |
YEATS2 |
1.7103e-06 |
1.2380e-06 |
1.3815 |
0.187362243 |
0.9694104 |
| 227 |
CTD.2047H16.2 |
4.8039e-06 |
3.5068e-06 |
1.3699 |
0.190884033 |
0.9694104 |
| 19 |
OAS1 |
2.7651e-06 |
2.0212e-06 |
1.3681 |
0.191434312 |
0.9694104 |
| 89 |
TRIM21 |
1.9801e-06 |
1.4553e-06 |
1.3606 |
0.193737686 |
0.9694104 |
| 145 |
MOV10 |
-1.8118e-06 |
1.3541e-06 |
-1.3380 |
0.200838528 |
0.9694104 |
| 171 |
LGALS9 |
-3.0486e-06 |
2.3050e-06 |
-1.3226 |
0.205776781 |
0.9694104 |
| 119 |
SCARB2 |
2.3239e-06 |
1.7767e-06 |
1.3080 |
0.210569468 |
0.9694104 |
| 215 |
CARD16 |
2.8097e-06 |
2.1505e-06 |
1.3065 |
0.211063124 |
0.9694104 |
| 157 |
CTSS |
-1.6600e-06 |
1.2775e-06 |
-1.2994 |
0.213410706 |
0.9694104 |
| 90 |
TRIM5 |
-2.2210e-06 |
1.7094e-06 |
-1.2993 |
0.213451856 |
0.9694104 |
| 228 |
RP3.508I15.21 |
-2.9880e-06 |
2.3086e-06 |
-1.2943 |
0.215144121 |
0.9694104 |
| 31 |
MYL12A |
2.4404e-06 |
1.8899e-06 |
1.2913 |
0.216140875 |
0.9694104 |
| 91 |
TRIM22 |
3.4477e-06 |
2.7726e-06 |
1.2435 |
0.232771521 |
0.9694104 |
| 94 |
EPSTI1 |
3.2421e-06 |
2.6198e-06 |
1.2375 |
0.234909719 |
0.9694104 |
| 58 |
GCA |
2.2824e-06 |
1.8728e-06 |
1.2187 |
0.241772396 |
0.9694104 |
| 109 |
STX17 |
-8.7470e-07 |
7.2210e-07 |
-1.2112 |
0.244556584 |
0.9694104 |
| 135 |
RASGRP3 |
2.0003e-06 |
1.6582e-06 |
1.2063 |
0.246387400 |
0.9694104 |
| 138 |
UTRN |
-1.3329e-06 |
1.1087e-06 |
-1.2022 |
0.247919584 |
0.9694104 |
| 196 |
ANKFY1 |
-1.7091e-06 |
1.4311e-06 |
-1.1942 |
0.250940977 |
0.9694104 |
| 69 |
MASTL |
-1.2759e-06 |
1.0769e-06 |
-1.1848 |
0.254516667 |
0.9694104 |
| 144 |
USP25 |
1.3552e-06 |
1.1661e-06 |
1.1622 |
0.263315242 |
0.9694104 |
| 64 |
ECE1 |
-2.1483e-06 |
1.8540e-06 |
-1.1587 |
0.264679757 |
0.9694104 |
| 5 |
SLC38A5 |
-2.7131e-06 |
2.3545e-06 |
-1.1523 |
0.267225821 |
0.9694104 |
| 118 |
HERC5 |
3.6168e-06 |
3.1919e-06 |
1.1331 |
0.274952710 |
0.9694104 |
| 4 |
NUB1 |
-1.2674e-06 |
1.1373e-06 |
-1.1144 |
0.282642236 |
0.9694104 |
| 105 |
CHST12 |
-1.7359e-06 |
1.5975e-06 |
-1.0866 |
0.294350779 |
0.9694104 |
| 141 |
SLFN13 |
-2.0915e-06 |
1.9457e-06 |
-1.0749 |
0.299400059 |
0.9694104 |
| 223 |
APOBEC3G |
2.3236e-06 |
2.1834e-06 |
1.0642 |
0.304060607 |
0.9694104 |
| 163 |
DTX3L |
-2.0650e-06 |
1.9452e-06 |
-1.0616 |
0.305221078 |
0.9694104 |
| 161 |
AIM2 |
3.2349e-06 |
3.0661e-06 |
1.0551 |
0.308090233 |
0.9694104 |
| 95 |
C14orf159 |
5.9700e-07 |
5.6850e-07 |
1.0502 |
0.310267094 |
0.9694104 |
| 40 |
TRIM14 |
-1.2050e-06 |
1.1524e-06 |
-1.0456 |
0.312296006 |
0.9694104 |
| 82 |
HELB |
-2.4039e-06 |
2.3295e-06 |
-1.0319 |
0.318469673 |
0.9694104 |
| 190 |
UBA7 |
-1.7696e-06 |
1.7173e-06 |
-1.0304 |
0.319138057 |
0.9694104 |
| 48 |
MDK |
-1.5921e-06 |
1.5499e-06 |
-1.0272 |
0.320606604 |
0.9694104 |
| 123 |
SECTM1 |
-2.6281e-06 |
2.5628e-06 |
-1.0255 |
0.321377661 |
0.9694104 |
| 44 |
KPNB1 |
-1.3842e-06 |
1.3533e-06 |
-1.0228 |
0.322622537 |
0.9694104 |
| 27 |
REC8 |
2.3933e-06 |
2.3763e-06 |
1.0071 |
0.329834433 |
0.9694104 |
| 146 |
UBE2L6 |
2.6362e-06 |
2.6227e-06 |
1.0052 |
0.330764136 |
0.9694104 |
| 125 |
PMAIP1 |
2.1055e-06 |
2.1193e-06 |
0.9935 |
0.336218007 |
0.9694104 |
| 148 |
ADPGK |
1.5633e-06 |
1.5855e-06 |
0.9860 |
0.339770004 |
0.9694104 |
| 35 |
N4BP1 |
-8.9720e-07 |
9.1840e-07 |
-0.9769 |
0.344116771 |
0.9694104 |
| 136 |
GPR180 |
1.6060e-06 |
1.6473e-06 |
0.9749 |
0.345061688 |
0.9694104 |
| 169 |
TRANK1 |
1.4388e-06 |
1.5409e-06 |
0.9337 |
0.365243291 |
0.9694104 |
| 167 |
SLFN5 |
3.2431e-06 |
3.5031e-06 |
0.9258 |
0.369215229 |
0.9694104 |
| 221 |
AC074338.4 |
1.6504e-06 |
1.7870e-06 |
0.9236 |
0.370336663 |
0.9694104 |
| 37 |
PRKD2 |
-1.6626e-06 |
1.8073e-06 |
-0.9199 |
0.372169663 |
0.9694104 |
| 45 |
LGALS3BP |
-1.3853e-06 |
1.5537e-06 |
-0.8916 |
0.386695942 |
0.9694104 |
| 46 |
DHX58 |
1.7813e-06 |
2.0180e-06 |
0.8827 |
0.391330703 |
0.9694104 |
| 108 |
CBWD2 |
-1.2238e-06 |
1.3914e-06 |
-0.8796 |
0.392972774 |
0.9694104 |
| 3 |
ETV7 |
3.2521e-06 |
3.7676e-06 |
0.8632 |
0.401631887 |
0.9694104 |
| 80 |
RBCK1 |
-1.7221e-06 |
2.0195e-06 |
-0.8527 |
0.407220386 |
0.9694104 |
| 10 |
TNK2 |
1.1807e-06 |
1.3860e-06 |
0.8519 |
0.407682210 |
0.9694104 |
| 14 |
DAPP1 |
2.1261e-06 |
2.4999e-06 |
0.8505 |
0.408427392 |
0.9694104 |
| 38 |
C1GALT1 |
1.2931e-06 |
1.5583e-06 |
0.8298 |
0.419663460 |
0.9694104 |
| 83 |
APOL2 |
2.6330e-06 |
3.1761e-06 |
0.8290 |
0.420100564 |
0.9694104 |
| 212 |
CARD11 |
2.2907e-06 |
2.7742e-06 |
0.8257 |
0.421887710 |
0.9694104 |
| 220 |
AC009950.2 |
-3.0621e-06 |
3.7182e-06 |
-0.8235 |
0.423110108 |
0.9694104 |
| 151 |
DBF4B |
-1.7741e-06 |
2.1615e-06 |
-0.8207 |
0.424640836 |
0.9694104 |
| 56 |
FRMD4B |
-1.2140e-06 |
1.4940e-06 |
-0.8126 |
0.429175893 |
0.9694104 |
| 127 |
IFITM3 |
-3.2773e-06 |
4.0599e-06 |
-0.8072 |
0.432153198 |
0.9694104 |
| 55 |
XRN1 |
-9.3110e-07 |
1.1550e-06 |
-0.8061 |
0.432763063 |
0.9694104 |
| 155 |
GBP4 |
2.9504e-06 |
3.7469e-06 |
0.7874 |
0.443290879 |
0.9694104 |
| 29 |
LPIN2 |
8.9260e-07 |
1.1507e-06 |
0.7757 |
0.449994061 |
0.9694104 |
| 193 |
USP18 |
-3.8446e-06 |
5.0005e-06 |
-0.7688 |
0.453918801 |
0.9694104 |
| 54 |
FAM46A |
-8.5110e-07 |
1.1231e-06 |
-0.7578 |
0.460314057 |
0.9694104 |
| 202 |
PLSCR1 |
1.1267e-06 |
1.4878e-06 |
0.7573 |
0.460589602 |
0.9694104 |
| 207 |
PGAP1 |
1.3407e-06 |
1.8041e-06 |
0.7431 |
0.468879462 |
0.9694104 |
| 67 |
IFIT2 |
2.7442e-06 |
3.7111e-06 |
0.7395 |
0.471041407 |
0.9694104 |
| 74 |
NT5C3A |
1.3953e-06 |
1.9226e-06 |
0.7257 |
0.479192879 |
0.9694104 |
| 86 |
BST2 |
-2.6535e-06 |
3.7922e-06 |
-0.6997 |
0.494807090 |
0.9694104 |
| 175 |
STAT2 |
-1.4173e-06 |
2.0471e-06 |
-0.6923 |
0.499312036 |
0.9694104 |
| 201 |
FANCA |
-1.2527e-06 |
1.8332e-06 |
-0.6834 |
0.504801843 |
0.9694104 |
| 230 |
RP11.640L9.2 |
-6.6100e-07 |
9.7140e-07 |
-0.6805 |
0.506585191 |
0.9694104 |
| 1 |
LAP3 |
-1.7551e-06 |
2.5923e-06 |
-0.6771 |
0.508675322 |
0.9694104 |
| 23 |
NANS |
-5.2490e-07 |
7.8290e-07 |
-0.6704 |
0.512799022 |
0.9694104 |
| 22 |
PSME1 |
-8.1840e-07 |
1.2211e-06 |
-0.6702 |
0.512891066 |
0.9694104 |
| 77 |
ZNFX1 |
-2.0604e-06 |
3.1460e-06 |
-0.6549 |
0.522423491 |
0.9694104 |
| 194 |
IFITM2 |
-2.1620e-06 |
3.3253e-06 |
-0.6502 |
0.525408478 |
0.9694104 |
| 183 |
CNP |
-7.8560e-07 |
1.2109e-06 |
-0.6488 |
0.526290851 |
0.9694104 |
| 92 |
XAF1 |
-2.3243e-06 |
3.5980e-06 |
-0.6460 |
0.528047992 |
0.9694104 |
| 21 |
RGS1 |
2.0129e-06 |
3.1895e-06 |
0.6311 |
0.537466754 |
0.9694104 |
| 68 |
CD274 |
2.3761e-06 |
3.8925e-06 |
0.6104 |
0.550716176 |
0.9694104 |
| 170 |
TTC21A |
-8.7300e-07 |
1.4427e-06 |
-0.6051 |
0.554151171 |
0.9694104 |
| 174 |
TRIM56 |
-1.0130e-06 |
1.6896e-06 |
-0.5996 |
0.557746348 |
0.9694104 |
| 87 |
HELZ2 |
1.4088e-06 |
2.3689e-06 |
0.5947 |
0.560896273 |
0.9694104 |
| 188 |
PARP10 |
-1.5040e-06 |
2.5737e-06 |
-0.5844 |
0.567647135 |
0.9694104 |
| 205 |
HSH2D |
1.1528e-06 |
1.9760e-06 |
0.5834 |
0.568299401 |
0.9694104 |
| 60 |
IL18R1 |
6.6870e-07 |
1.1789e-06 |
0.5672 |
0.578978094 |
0.9694104 |
| 112 |
CASP1 |
1.4077e-06 |
2.4939e-06 |
0.5644 |
0.580798434 |
0.9694104 |
| 26 |
PSME2 |
-1.3640e-06 |
2.4560e-06 |
-0.5554 |
0.586824348 |
0.9694104 |
| 218 |
APOL6 |
9.1320e-07 |
1.6826e-06 |
0.5427 |
0.595293184 |
0.9694104 |
| 226 |
RP11.468E2.4 |
-1.4127e-06 |
2.6595e-06 |
-0.5312 |
0.603071179 |
0.9694104 |
| 120 |
BRCA2 |
-8.7090e-07 |
1.6447e-06 |
-0.5295 |
0.604175931 |
0.9694104 |
| 71 |
TRIM25 |
1.2013e-06 |
2.2854e-06 |
0.5256 |
0.606823271 |
0.9694104 |
| 47 |
UNC93B1 |
-9.8950e-07 |
1.8829e-06 |
-0.5255 |
0.606905546 |
0.9694104 |
| 98 |
OASL |
1.4809e-06 |
2.8675e-06 |
0.5164 |
0.613074479 |
0.9694104 |
| 209 |
C5orf56 |
1.0472e-06 |
2.0649e-06 |
0.5071 |
0.619428053 |
0.9694104 |
| 176 |
GIMAP8 |
8.6130e-07 |
1.7145e-06 |
0.5024 |
0.622708582 |
0.9694104 |
| 9 |
PARP12 |
6.0400e-07 |
1.2115e-06 |
0.4985 |
0.625347956 |
0.9694104 |
| 79 |
MT2A |
1.3086e-06 |
2.6557e-06 |
0.4928 |
0.629312953 |
0.9694104 |
| 134 |
SCLT1 |
4.9980e-07 |
1.0188e-06 |
0.4906 |
0.630796979 |
0.9694104 |
| 208 |
GTF2E2 |
-2.9010e-07 |
5.9320e-07 |
-0.4890 |
0.631893236 |
0.9694104 |
| 66 |
IFIT3 |
2.7502e-06 |
5.6960e-06 |
0.4828 |
0.636189331 |
0.9694104 |
| 147 |
MX1 |
-2.3317e-06 |
4.8445e-06 |
-0.4813 |
0.637236308 |
0.9694104 |
| 173 |
BUB1 |
8.3300e-07 |
1.7533e-06 |
0.4751 |
0.641548517 |
0.9694104 |
| 229 |
AC008079.10 |
1.2308e-06 |
2.6187e-06 |
0.4700 |
0.645109888 |
0.9694104 |
| 36 |
EHD4 |
-5.3770e-07 |
1.1584e-06 |
-0.4641 |
0.649221959 |
0.9694104 |
| 198 |
TRIM69 |
-9.1700e-07 |
1.9863e-06 |
-0.4617 |
0.650955688 |
0.9694104 |
| 117 |
HERC6 |
-1.6512e-06 |
3.5801e-06 |
-0.4612 |
0.651262664 |
0.9694104 |
| 179 |
ISG20 |
1.1154e-06 |
2.4509e-06 |
0.4551 |
0.655548741 |
0.9694104 |
| 33 |
TNFSF13B |
-1.0552e-06 |
2.3196e-06 |
-0.4549 |
0.655700284 |
0.9694104 |
| 41 |
DDX58 |
1.3575e-06 |
3.0115e-06 |
0.4508 |
0.658606508 |
0.9694104 |
| 128 |
MCL1 |
1.0790e-06 |
2.4384e-06 |
0.4425 |
0.664457971 |
0.9694104 |
| 162 |
PPM1K |
8.3700e-07 |
1.8935e-06 |
0.4420 |
0.664766919 |
0.9694104 |
| 156 |
CAPN2 |
-4.7850e-07 |
1.0842e-06 |
-0.4414 |
0.665239879 |
0.9694104 |
| 85 |
SAT1 |
3.8890e-07 |
9.0730e-07 |
0.4287 |
0.674256982 |
0.9694104 |
| 107 |
TANK |
4.6280e-07 |
1.0951e-06 |
0.4226 |
0.678572548 |
0.9694104 |
| 17 |
DNAJA1 |
5.9000e-07 |
1.4161e-06 |
0.4166 |
0.682847117 |
0.9694104 |
| 103 |
PHF11 |
4.7870e-07 |
1.1547e-06 |
0.4145 |
0.684346068 |
0.9694104 |
| 160 |
IFI16 |
9.6740e-07 |
2.3361e-06 |
0.4141 |
0.684652245 |
0.9694104 |
| 129 |
SLC18B1 |
3.0450e-07 |
7.7780e-07 |
0.3914 |
0.700984714 |
0.9694104 |
| 200 |
ISG15 |
-1.9897e-06 |
5.1164e-06 |
-0.3889 |
0.702824378 |
0.9694104 |
| 225 |
RP11.81H14.2 |
7.4410e-07 |
1.9163e-06 |
0.3883 |
0.703251960 |
0.9694104 |
| 61 |
FBXO6 |
-1.0422e-06 |
2.7657e-06 |
-0.3768 |
0.711575057 |
0.9694104 |
| 216 |
SAMD9 |
-6.6170e-07 |
1.8261e-06 |
-0.3624 |
0.722130410 |
0.9694104 |
| 81 |
IFI6 |
-2.1696e-06 |
6.1312e-06 |
-0.3539 |
0.728361522 |
0.9694104 |
| 192 |
RBM43 |
4.6250e-07 |
1.3098e-06 |
0.3531 |
0.728903223 |
0.9694104 |
| 204 |
SPATS2L |
-2.1390e-07 |
6.1170e-07 |
-0.3498 |
0.731381088 |
0.9694104 |
| 12 |
SP100 |
-5.4410e-07 |
1.5630e-06 |
-0.3481 |
0.732612113 |
0.9694104 |
| 206 |
CASP4 |
-5.8400e-07 |
1.7454e-06 |
-0.3346 |
0.742563833 |
0.9694104 |
| 65 |
BLZF1 |
-3.4590e-07 |
1.0601e-06 |
-0.3263 |
0.748691388 |
0.9694104 |
| 101 |
USP15 |
-2.6290e-07 |
8.1550e-07 |
-0.3224 |
0.751631140 |
0.9694104 |
| 59 |
STAT1 |
7.4490e-07 |
2.3435e-06 |
0.3179 |
0.754965125 |
0.9694104 |
| 96 |
RSAD2 |
-1.4066e-06 |
4.4812e-06 |
-0.3139 |
0.757930266 |
0.9694104 |
| 76 |
NMI |
4.9110e-07 |
1.6022e-06 |
0.3065 |
0.763419411 |
0.9694104 |
| 2 |
CD38 |
8.4820e-07 |
2.7992e-06 |
0.3030 |
0.766036072 |
0.9694104 |
| 20 |
LAG3 |
-1.1289e-06 |
3.7963e-06 |
-0.2974 |
0.770266807 |
0.9694104 |
| 115 |
PNPT1 |
-6.7720e-07 |
2.3121e-06 |
-0.2929 |
0.773608600 |
0.9694104 |
| 24 |
JAK2 |
-3.8440e-07 |
1.3149e-06 |
-0.2924 |
0.774019928 |
0.9694104 |
| 168 |
NOD2 |
5.0660e-07 |
1.7702e-06 |
0.2862 |
0.778651265 |
0.9694104 |
| 8 |
EIF2AK2 |
4.5270e-07 |
1.6533e-06 |
0.2738 |
0.787978946 |
0.9694104 |
| 50 |
OAS3 |
9.9180e-07 |
3.7190e-06 |
0.2667 |
0.793345866 |
0.9694104 |
| 153 |
RAVER2 |
4.8430e-07 |
1.9111e-06 |
0.2534 |
0.803409849 |
0.9694104 |
| 197 |
IFIT1 |
1.2816e-06 |
5.1241e-06 |
0.2501 |
0.805886347 |
0.9694104 |
| 104 |
SETDB2 |
-1.5500e-07 |
6.2500e-07 |
-0.2480 |
0.807459944 |
0.9694104 |
| 132 |
STOM |
-5.5460e-07 |
2.2855e-06 |
-0.2427 |
0.811561758 |
0.9694104 |
| 63 |
GBP1 |
9.8060e-07 |
4.0482e-06 |
0.2422 |
0.811883750 |
0.9694104 |
| 43 |
LIPA |
6.3400e-07 |
2.6834e-06 |
0.2363 |
0.816409077 |
0.9694104 |
| 186 |
SAMD9L |
7.0160e-07 |
2.9882e-06 |
0.2348 |
0.817551119 |
0.9694104 |
| 195 |
IRF7 |
7.5780e-07 |
3.2401e-06 |
0.2339 |
0.818240146 |
0.9694104 |
| 102 |
SP110 |
4.8750e-07 |
2.1070e-06 |
0.2314 |
0.820155357 |
0.9694104 |
| 28 |
SAMHD1 |
-5.9420e-07 |
2.6938e-06 |
-0.2206 |
0.828403397 |
0.9694104 |
| 166 |
IFI27 |
-5.7200e-07 |
2.5978e-06 |
-0.2202 |
0.828694211 |
0.9694104 |
| 113 |
IFI44L |
-1.3133e-06 |
6.1210e-06 |
-0.2146 |
0.833006194 |
0.9694104 |
| 111 |
DDX60 |
-4.4100e-07 |
2.1145e-06 |
-0.2086 |
0.837591422 |
0.9694104 |
| 159 |
AZI2 |
1.5960e-07 |
7.7360e-07 |
0.2063 |
0.839326357 |
0.9694104 |
| 13 |
IFI35 |
4.9950e-07 |
2.5552e-06 |
0.1955 |
0.847625713 |
0.9694104 |
| 184 |
RNF213 |
4.6010e-07 |
2.4371e-06 |
0.1888 |
0.852797528 |
0.9694104 |
| 149 |
ADAR |
2.0180e-07 |
1.0810e-06 |
0.1867 |
0.854421647 |
0.9694104 |
| 78 |
ZBP1 |
-6.2410e-07 |
3.4306e-06 |
-0.1819 |
0.858087399 |
0.9694104 |
| 88 |
C19orf66 |
-3.1910e-07 |
1.7546e-06 |
-0.1818 |
0.858147129 |
0.9694104 |
| 93 |
ALOX5AP |
3.0180e-07 |
1.6759e-06 |
0.1801 |
0.859476794 |
0.9694104 |
| 224 |
PSMB9 |
-5.4380e-07 |
3.0432e-06 |
-0.1787 |
0.860563274 |
0.9694104 |
| 114 |
IFI44 |
8.4100e-07 |
4.9857e-06 |
0.1687 |
0.868302678 |
0.9694104 |
| 152 |
AK4 |
1.3550e-07 |
8.0550e-07 |
0.1682 |
0.868655172 |
0.9694104 |
| 72 |
TNFSF10 |
-3.8940e-07 |
2.3434e-06 |
-0.1662 |
0.870256630 |
0.9694104 |
| 187 |
ODF3B |
-4.5140e-07 |
2.8756e-06 |
-0.1570 |
0.877358650 |
0.9694104 |
| 49 |
PARP11 |
1.6990e-07 |
1.0900e-06 |
0.1559 |
0.878191334 |
0.9694104 |
| 154 |
NEXN |
1.9680e-07 |
1.2678e-06 |
0.1552 |
0.878698052 |
0.9694104 |
| 121 |
PML |
-3.9640e-07 |
2.6247e-06 |
-0.1510 |
0.881971075 |
0.9694104 |
| 150 |
LY6E |
-5.3990e-07 |
3.7327e-06 |
-0.1446 |
0.886922801 |
0.9694104 |
| 16 |
SP140 |
-4.5080e-07 |
3.1182e-06 |
-0.1446 |
0.886963785 |
0.9694104 |
| 189 |
DDX60L |
-3.9040e-07 |
2.7210e-06 |
-0.1435 |
0.887813732 |
0.9694104 |
| 219 |
GBP1P1 |
-6.7910e-07 |
4.8186e-06 |
-0.1409 |
0.889797353 |
0.9694104 |
| 185 |
DRAP1 |
1.8170e-07 |
1.3847e-06 |
0.1312 |
0.897362378 |
0.9694104 |
| 97 |
CMPK2 |
4.6970e-07 |
3.7269e-06 |
0.1260 |
0.901388972 |
0.9694104 |
| 34 |
PARP4 |
7.8600e-08 |
6.9290e-07 |
0.1135 |
0.911176290 |
0.9694104 |
| 51 |
OAS2 |
-4.9310e-07 |
4.3628e-06 |
-0.1130 |
0.911510354 |
0.9694104 |
| 15 |
IPCEF1 |
1.4280e-07 |
1.3441e-06 |
0.1062 |
0.916803485 |
0.9694104 |
| 57 |
IFIH1 |
2.8460e-07 |
2.6836e-06 |
0.1061 |
0.916936647 |
0.9694104 |
| 139 |
MCOLN2 |
-2.9550e-07 |
2.8516e-06 |
-0.1036 |
0.918832481 |
0.9694104 |
| 199 |
C11orf96 |
-2.5320e-07 |
2.7645e-06 |
-0.0916 |
0.928224353 |
0.9748475 |
| 42 |
SETX |
6.0700e-08 |
7.0800e-07 |
0.0857 |
0.932848565 |
0.9752508 |
| 75 |
ACO1 |
-4.5600e-08 |
9.1840e-07 |
-0.0496 |
0.961081034 |
0.9901315 |
| 182 |
PARP14 |
1.1940e-07 |
2.5983e-06 |
0.0459 |
0.963960516 |
0.9901315 |
| 62 |
GBP3 |
1.1040e-07 |
2.4958e-06 |
0.0442 |
0.965302868 |
0.9901315 |
| 217 |
IRF9 |
1.1640e-07 |
2.8617e-06 |
0.0407 |
0.968083427 |
0.9901315 |
| 172 |
IRS1 |
-4.5500e-08 |
1.1367e-06 |
-0.0400 |
0.968606948 |
0.9901315 |
| 6 |
TYMP |
-7.0100e-08 |
3.9543e-06 |
-0.0177 |
0.986079935 |
0.9970929 |
| 140 |
GBP5 |
6.0100e-08 |
4.7043e-06 |
0.0128 |
0.989979569 |
0.9970929 |
| 25 |
APOL1 |
-3.0900e-08 |
3.2844e-06 |
-0.0094 |
0.992617645 |
0.9970929 |
| 191 |
MX2 |
-1.8100e-08 |
4.6008e-06 |
-0.0039 |
0.996906239 |
0.9970929 |
| 122 |
NLRC5 |
9.0000e-09 |
2.4308e-06 |
0.0037 |
0.997092893 |
0.9970929 |
## betas
gene_FunReg(as.matrix(genesbeta.rld.lin[, 2:424]), genesbeta.rld.lin[,
428], "IFN-beta Genes", "Plasma Viral Load")
Top Genes from IFN-beta Genes Associated with Outcome: Plasma Viral Load by p.value (Sample Size = NA)
| 15 |
THOC3 |
8.16970e-06 |
2.1273e-06 |
3.8404 |
0.001604998 |
0.2120574 |
| 146 |
INO80 |
3.95000e-06 |
1.0703e-06 |
3.6905 |
0.002180955 |
0.2120574 |
| 64 |
CCNB1IP1 |
4.38260e-06 |
1.2289e-06 |
3.5664 |
0.002813188 |
0.2120574 |
| 256 |
RPL30 |
8.95710e-06 |
2.6573e-06 |
3.3707 |
0.004202861 |
0.2120574 |
| 234 |
SLC25A4 |
3.38200e-06 |
1.0124e-06 |
3.3404 |
0.004472326 |
0.2120574 |
| 181 |
CENPO |
4.77840e-06 |
1.4430e-06 |
3.3115 |
0.004746018 |
0.2120574 |
| 420 |
LIX1L |
1.01495e-05 |
3.1354e-06 |
3.2371 |
0.005527284 |
0.2120574 |
| 253 |
PXYLP1 |
5.85940e-06 |
1.8224e-06 |
3.2152 |
0.005781029 |
0.2120574 |
| 407 |
ALG13.AS1 |
7.63880e-06 |
2.3837e-06 |
3.2045 |
0.005908588 |
0.2120574 |
| 123 |
PLEKHG1 |
7.57930e-06 |
2.4263e-06 |
3.1238 |
0.006970559 |
0.2120574 |
| 252 |
FZD7 |
6.67650e-06 |
2.1498e-06 |
3.1056 |
0.007233850 |
0.2120574 |
| 292 |
AQP3 |
1.34789e-05 |
4.3732e-06 |
3.0821 |
0.007589009 |
0.2120574 |
| 149 |
ZNF227 |
8.43510e-06 |
2.7846e-06 |
3.0292 |
0.008454548 |
0.2120574 |
| 194 |
KANSL2 |
6.04800e-06 |
2.0325e-06 |
2.9757 |
0.009427176 |
0.2120574 |
| 175 |
CCDC90B |
5.34980e-06 |
1.8182e-06 |
2.9424 |
0.010088503 |
0.2120574 |
| 148 |
TAF4 |
3.26670e-06 |
1.1609e-06 |
2.8139 |
0.013088513 |
0.2120574 |
| 364 |
RPS23 |
7.86390e-06 |
2.8050e-06 |
2.8035 |
0.013363791 |
0.2120574 |
| 119 |
RPS25 |
7.27780e-06 |
2.6190e-06 |
2.7788 |
0.014047395 |
0.2120574 |
| 193 |
N4BP2L1 |
4.71760e-06 |
1.7211e-06 |
2.7411 |
0.015156148 |
0.2120574 |
| 214 |
LRIG1 |
5.07810e-06 |
1.8589e-06 |
2.7317 |
0.015443272 |
0.2120574 |
| 4 |
UFL1 |
1.45140e-06 |
5.3280e-07 |
2.7244 |
0.015671760 |
0.2120574 |
| 10 |
GRN |
-3.55480e-06 |
1.3096e-06 |
-2.7145 |
0.015986286 |
0.2120574 |
| 406 |
LINC00623 |
5.92900e-06 |
2.2075e-06 |
2.6859 |
0.016931359 |
0.2120574 |
| 136 |
BTN2A2 |
4.98510e-06 |
1.8799e-06 |
2.6518 |
0.018126835 |
0.2120574 |
| 55 |
SLC23A2 |
7.19130e-06 |
2.7409e-06 |
2.6237 |
0.019173505 |
0.2120574 |
| 262 |
SLC35B2 |
9.36520e-06 |
3.5971e-06 |
2.6035 |
0.019957500 |
0.2120574 |
| 322 |
PPP1CA |
1.09779e-05 |
4.2179e-06 |
2.6027 |
0.019990849 |
0.2120574 |
| 60 |
HNRNPH3 |
5.85750e-06 |
2.2539e-06 |
2.5988 |
0.020147286 |
0.2120574 |
| 127 |
SERP1 |
2.41280e-06 |
9.2920e-07 |
2.5967 |
0.020230307 |
0.2120574 |
| 341 |
C8orf59 |
3.03300e-06 |
1.1766e-06 |
2.5777 |
0.021012088 |
0.2120574 |
| 359 |
CSF1 |
5.06860e-06 |
1.9843e-06 |
2.5544 |
0.022006146 |
0.2120574 |
| 8 |
IFNGR1 |
6.57860e-06 |
2.5888e-06 |
2.5411 |
0.022591048 |
0.2120574 |
| 141 |
SHFM1 |
7.10040e-06 |
2.8023e-06 |
2.5338 |
0.022921277 |
0.2120574 |
| 366 |
GTF2F2 |
3.17900e-06 |
1.2569e-06 |
2.5293 |
0.023125894 |
0.2120574 |
| 370 |
PNRC2 |
1.91890e-06 |
7.6230e-07 |
2.5174 |
0.023679204 |
0.2120574 |
| 54 |
DOCK9 |
6.01100e-06 |
2.3993e-06 |
2.5053 |
0.024249274 |
0.2120574 |
| 101 |
C5orf15 |
1.10474e-05 |
4.4171e-06 |
2.5011 |
0.024454105 |
0.2120574 |
| 332 |
HOXB2 |
6.04270e-06 |
2.4288e-06 |
2.4879 |
0.025095663 |
0.2120574 |
| 74 |
TMEM87A |
7.00950e-06 |
2.8292e-06 |
2.4776 |
0.025612899 |
0.2120574 |
| 421 |
GTF2H5 |
4.82680e-06 |
1.9488e-06 |
2.4768 |
0.025651107 |
0.2120574 |
| 327 |
TRMT112 |
1.07278e-05 |
4.3492e-06 |
2.4666 |
0.026172011 |
0.2120574 |
| 31 |
ARFGEF1 |
3.95820e-06 |
1.6067e-06 |
2.4635 |
0.026333254 |
0.2120574 |
| 110 |
KDM3A |
2.80060e-06 |
1.1438e-06 |
2.4485 |
0.027122151 |
0.2120574 |
| 245 |
MRPL39 |
6.88330e-06 |
2.8209e-06 |
2.4401 |
0.027572118 |
0.2120574 |
| 20 |
ATG5 |
5.19560e-06 |
2.1300e-06 |
2.4392 |
0.027620701 |
0.2120574 |
| 270 |
BSDC1 |
4.14290e-06 |
1.7033e-06 |
2.4323 |
0.027999339 |
0.2120574 |
| 69 |
POFUT1 |
4.12320e-06 |
1.6996e-06 |
2.4260 |
0.028346229 |
0.2120574 |
| 416 |
NBPF11 |
6.32000e-06 |
2.6114e-06 |
2.4201 |
0.028674028 |
0.2120574 |
| 189 |
PEX5 |
8.02040e-06 |
3.3575e-06 |
2.3888 |
0.030483764 |
0.2120574 |
| 226 |
EBAG9 |
1.35210e-06 |
5.6920e-07 |
2.3755 |
0.031283332 |
0.2120574 |
| 188 |
KIF21A |
3.53700e-06 |
1.4958e-06 |
2.3647 |
0.031950968 |
0.2120574 |
| 216 |
ATG3 |
2.13250e-06 |
9.0500e-07 |
2.3562 |
0.032482342 |
0.2120574 |
| 79 |
INTS10 |
3.55660e-06 |
1.5120e-06 |
2.3522 |
0.032735615 |
0.2120574 |
| 381 |
UCKL1 |
7.11860e-06 |
3.0321e-06 |
2.3478 |
0.033020643 |
0.2120574 |
| 244 |
TCEB1 |
4.09510e-06 |
1.7516e-06 |
2.3379 |
0.033662550 |
0.2120574 |
| 99 |
ARSB |
5.44070e-06 |
2.3346e-06 |
2.3305 |
0.034150077 |
0.2120574 |
| 58 |
CMTM6 |
1.00451e-05 |
4.3110e-06 |
2.3301 |
0.034172309 |
0.2120574 |
| 124 |
PROSER1 |
5.39580e-06 |
2.3235e-06 |
2.3223 |
0.034695553 |
0.2120574 |
| 325 |
ZNF680 |
5.46040e-06 |
2.3532e-06 |
2.3204 |
0.034823068 |
0.2120574 |
| 282 |
RPN1 |
5.41080e-06 |
2.3343e-06 |
2.3179 |
0.034990110 |
0.2120574 |
| 333 |
C16orf91 |
7.46410e-06 |
3.2224e-06 |
2.3164 |
0.035096214 |
0.2120574 |
| 277 |
EIF4E3 |
4.66260e-06 |
2.0211e-06 |
2.3069 |
0.035742405 |
0.2120574 |
| 365 |
COMMD6 |
9.51670e-06 |
4.1315e-06 |
2.3035 |
0.035983200 |
0.2120574 |
| 142 |
LSM8 |
2.11480e-06 |
9.2020e-07 |
2.2981 |
0.036355989 |
0.2120574 |
| 68 |
TM9SF4 |
1.92770e-06 |
8.3900e-07 |
2.2976 |
0.036394413 |
0.2120574 |
| 116 |
SWT1 |
3.54120e-06 |
1.5427e-06 |
2.2955 |
0.036541927 |
0.2120574 |
| 392 |
C1orf174 |
9.45660e-06 |
4.1261e-06 |
2.2919 |
0.036795000 |
0.2120574 |
| 240 |
TXNDC11 |
4.74030e-06 |
2.0720e-06 |
2.2878 |
0.037088550 |
0.2120574 |
| 24 |
MTMR1 |
4.33670e-06 |
1.8959e-06 |
2.2874 |
0.037119155 |
0.2120574 |
| 345 |
ARL6IP6 |
2.74320e-06 |
1.2023e-06 |
2.2817 |
0.037529831 |
0.2120574 |
| 268 |
UBR1 |
3.58950e-06 |
1.5804e-06 |
2.2712 |
0.038293995 |
0.2120574 |
| 138 |
L3HYPDH |
6.95920e-06 |
3.0684e-06 |
2.2680 |
0.038531549 |
0.2120574 |
| 402 |
CLIC1 |
7.52420e-06 |
3.3277e-06 |
2.2611 |
0.039048893 |
0.2120574 |
| 274 |
NCSTN |
9.31290e-06 |
4.1291e-06 |
2.2555 |
0.039472249 |
0.2120574 |
| 225 |
LACTB2 |
3.98180e-06 |
1.7685e-06 |
2.2515 |
0.039776073 |
0.2120574 |
| 338 |
EIF1AD |
6.78850e-06 |
3.0307e-06 |
2.2399 |
0.040670109 |
0.2120574 |
| 38 |
SCARF1 |
7.10820e-06 |
3.1781e-06 |
2.2366 |
0.040923345 |
0.2120574 |
| 30 |
ISOC1 |
8.57770e-06 |
3.8447e-06 |
2.2311 |
0.041364205 |
0.2120574 |
| 207 |
INTS7 |
3.47530e-06 |
1.5652e-06 |
2.2204 |
0.042220727 |
0.2120574 |
| 130 |
B4GALT4 |
8.30830e-06 |
3.7523e-06 |
2.2142 |
0.042722876 |
0.2120574 |
| 152 |
SEC61G |
8.97380e-06 |
4.0636e-06 |
2.2084 |
0.043200591 |
0.2120574 |
| 2 |
RANBP9 |
4.45960e-06 |
2.0199e-06 |
2.2078 |
0.043247731 |
0.2120574 |
| 305 |
NUDT21 |
6.87410e-06 |
3.1310e-06 |
2.1955 |
0.044276264 |
0.2120574 |
| 158 |
CYP2J2 |
6.23680e-06 |
2.8448e-06 |
2.1923 |
0.044543195 |
0.2120574 |
| 314 |
TM2D2 |
3.83080e-06 |
1.7528e-06 |
2.1856 |
0.045119984 |
0.2120574 |
| 198 |
GLYR1 |
2.29470e-06 |
1.0553e-06 |
2.1744 |
0.046090247 |
0.2120574 |
| 209 |
SRP9 |
7.85510e-06 |
3.6170e-06 |
2.1717 |
0.046325242 |
0.2120574 |
| 241 |
RPIA |
6.34740e-06 |
2.9249e-06 |
2.1702 |
0.046463426 |
0.2120574 |
| 399 |
NRAS |
9.52140e-06 |
4.4041e-06 |
2.1619 |
0.047194925 |
0.2120574 |
| 51 |
DDHD2 |
3.32130e-06 |
1.5393e-06 |
2.1577 |
0.047572634 |
0.2120574 |
| 404 |
LINC00998 |
5.56520e-06 |
2.5859e-06 |
2.1522 |
0.048077434 |
0.2120574 |
| 202 |
SMAD4 |
4.08460e-06 |
1.9064e-06 |
2.1426 |
0.048958866 |
0.2120574 |
| 351 |
IGIP |
7.19510e-06 |
3.3586e-06 |
2.1423 |
0.048987203 |
0.2120574 |
| 403 |
NAXD |
3.39640e-06 |
1.5885e-06 |
2.1381 |
0.049377704 |
0.2120574 |
| 143 |
IRF5 |
4.64790e-06 |
2.1772e-06 |
2.1348 |
0.049683781 |
0.2120574 |
| 291 |
KIAA0196 |
4.05850e-06 |
1.9210e-06 |
2.1127 |
0.051797504 |
0.2120574 |
| 296 |
QSOX2 |
4.09490e-06 |
1.9403e-06 |
2.1105 |
0.052019021 |
0.2120574 |
| 283 |
ANXA5 |
3.65880e-06 |
1.7350e-06 |
2.1088 |
0.052184865 |
0.2120574 |
| 199 |
SLC39A6 |
3.86670e-06 |
1.8351e-06 |
2.1071 |
0.052350204 |
0.2120574 |
| 289 |
SUN1 |
6.98530e-06 |
3.3226e-06 |
2.1023 |
0.052824245 |
0.2120574 |
| 284 |
FBXO8 |
4.55440e-06 |
2.1704e-06 |
2.0984 |
0.053215036 |
0.2120574 |
| 115 |
TMEM59 |
8.33060e-06 |
3.9742e-06 |
2.0961 |
0.053441814 |
0.2120574 |
| 367 |
FAM92A1 |
3.88360e-06 |
1.8570e-06 |
2.0913 |
0.053928611 |
0.2120574 |
| 89 |
BIN2 |
4.55310e-06 |
2.1849e-06 |
2.0839 |
0.054688556 |
0.2120574 |
| 97 |
COX7A2 |
3.25710e-06 |
1.5631e-06 |
2.0838 |
0.054696027 |
0.2120574 |
| 400 |
LEPROT |
2.29440e-06 |
1.1077e-06 |
2.0712 |
0.055998797 |
0.2120574 |
| 185 |
NUP54 |
2.90160e-06 |
1.4079e-06 |
2.0609 |
0.057094532 |
0.2120574 |
| 96 |
SMAP1 |
4.08070e-06 |
1.9852e-06 |
2.0556 |
0.057658829 |
0.2120574 |
| 227 |
MFSD14B |
6.82320e-06 |
3.3450e-06 |
2.0398 |
0.059382297 |
0.2120574 |
| 94 |
RWDD1 |
4.69750e-06 |
2.3057e-06 |
2.0374 |
0.059656236 |
0.2120574 |
| 47 |
PCNP |
3.52180e-06 |
1.7288e-06 |
2.0371 |
0.059689623 |
0.2120574 |
| 121 |
MYL12B |
5.06790e-06 |
2.4882e-06 |
2.0368 |
0.059723424 |
0.2120574 |
| 378 |
AKAP17A |
3.21980e-06 |
1.5860e-06 |
2.0301 |
0.060465476 |
0.2120574 |
| 323 |
MUS81 |
5.27190e-06 |
2.6010e-06 |
2.0269 |
0.060833835 |
0.2120574 |
| 260 |
AASDH |
4.86860e-06 |
2.4033e-06 |
2.0259 |
0.060949514 |
0.2120574 |
| 363 |
ZBTB6 |
3.34140e-06 |
1.6537e-06 |
2.0205 |
0.061553313 |
0.2120574 |
| 129 |
TNFRSF10B |
6.23720e-06 |
3.0950e-06 |
2.0153 |
0.062159058 |
0.2120574 |
| 261 |
DSCR3 |
3.82740e-06 |
1.9049e-06 |
2.0092 |
0.062859198 |
0.2120574 |
| 21 |
ALDH18A1 |
7.13270e-06 |
3.5609e-06 |
2.0031 |
0.063581362 |
0.2120574 |
| 28 |
OAT |
8.41770e-06 |
4.2113e-06 |
1.9988 |
0.064084776 |
0.2120574 |
| 221 |
BTF3 |
4.03970e-06 |
2.0213e-06 |
1.9986 |
0.064110950 |
0.2120574 |
| 187 |
USO1 |
2.11550e-06 |
1.0595e-06 |
1.9968 |
0.064329048 |
0.2120574 |
| 251 |
FAM126B |
6.30420e-06 |
3.1574e-06 |
1.9967 |
0.064341779 |
0.2120574 |
| 285 |
LSM6 |
4.19180e-06 |
2.1037e-06 |
1.9926 |
0.064827067 |
0.2120574 |
| 156 |
EMC7 |
5.48180e-06 |
2.7561e-06 |
1.9889 |
0.065268537 |
0.2120574 |
| 203 |
CREG1 |
4.36170e-06 |
2.1969e-06 |
1.9854 |
0.065697339 |
0.2120574 |
| 87 |
NDUFC1 |
6.40980e-06 |
3.2288e-06 |
1.9852 |
0.065723335 |
0.2120574 |
| 293 |
GTF2A1 |
6.11600e-06 |
3.0814e-06 |
1.9848 |
0.065766727 |
0.2120574 |
| 220 |
SRD5A1 |
3.64950e-06 |
1.8442e-06 |
1.9789 |
0.066483143 |
0.2120574 |
| 272 |
JAK1 |
1.93230e-06 |
9.7670e-07 |
1.9783 |
0.066560207 |
0.2120574 |
| 374 |
ZSCAN25 |
3.14790e-06 |
1.5962e-06 |
1.9722 |
0.067319898 |
0.2120574 |
| 165 |
CAB39 |
5.49780e-06 |
2.7880e-06 |
1.9720 |
0.067344155 |
0.2120574 |
| 369 |
ZNF548 |
3.73460e-06 |
1.8948e-06 |
1.9710 |
0.067460429 |
0.2120574 |
| 105 |
SF3B6 |
5.72200e-06 |
2.9031e-06 |
1.9710 |
0.067461820 |
0.2120574 |
| 84 |
EIF4H |
3.02740e-06 |
1.5373e-06 |
1.9693 |
0.067677898 |
0.2120574 |
| 107 |
LANCL1 |
3.88530e-06 |
1.9887e-06 |
1.9536 |
0.069654945 |
0.2155898 |
| 318 |
XKR6 |
4.92210e-06 |
2.5212e-06 |
1.9523 |
0.069824597 |
0.2155898 |
| 106 |
ACVR1 |
5.94100e-06 |
3.0529e-06 |
1.9461 |
0.070629741 |
0.2164955 |
| 184 |
VWA9 |
6.87480e-06 |
3.5507e-06 |
1.9362 |
0.071918901 |
0.2184966 |
| 316 |
ARL6IP1 |
6.26090e-06 |
3.2387e-06 |
1.9332 |
0.072315656 |
0.2184966 |
| 232 |
ACAD8 |
4.63080e-06 |
2.4055e-06 |
1.9251 |
0.073394168 |
0.2201825 |
| 195 |
RB1 |
5.82640e-06 |
3.0372e-06 |
1.9184 |
0.074301170 |
0.2213338 |
| 204 |
RFWD2 |
3.72150e-06 |
1.9506e-06 |
1.9079 |
0.075739303 |
0.2239953 |
| 81 |
BET1 |
1.53460e-06 |
8.0590e-07 |
1.9041 |
0.076253725 |
0.2239953 |
| 299 |
TRUB1 |
5.56770e-06 |
2.9376e-06 |
1.8953 |
0.077489460 |
0.2256728 |
| 267 |
BTG2 |
4.59830e-06 |
2.4305e-06 |
1.8919 |
0.077975559 |
0.2256728 |
| 19 |
HPF1 |
5.16820e-06 |
2.7400e-06 |
1.8862 |
0.078781446 |
0.2256728 |
| 391 |
CAPZA2 |
2.46000e-06 |
1.3084e-06 |
1.8802 |
0.079642215 |
0.2256728 |
| 145 |
PSMG2 |
4.46960e-06 |
2.3778e-06 |
1.8797 |
0.079709443 |
0.2256728 |
| 160 |
TMED7 |
4.10580e-06 |
2.1868e-06 |
1.8776 |
0.080025828 |
0.2256728 |
| 279 |
RPL22L1 |
7.14090e-06 |
3.8132e-06 |
1.8727 |
0.080736912 |
0.2261703 |
| 103 |
INO80D |
2.60980e-06 |
1.4009e-06 |
1.8629 |
0.082171886 |
0.2277222 |
| 144 |
MTX2 |
5.98250e-06 |
3.2196e-06 |
1.8582 |
0.082881387 |
0.2277222 |
| 306 |
GLOD4 |
2.31390e-06 |
1.2466e-06 |
1.8561 |
0.083185326 |
0.2277222 |
| 313 |
ZBTB49 |
4.57230e-06 |
2.4656e-06 |
1.8544 |
0.083444287 |
0.2277222 |
| 159 |
RNF138 |
5.85760e-06 |
3.1739e-06 |
1.8456 |
0.084783174 |
0.2277418 |
| 151 |
PRKAA1 |
3.84540e-06 |
2.0841e-06 |
1.8451 |
0.084851199 |
0.2277418 |
| 297 |
PRDX3 |
7.37400e-06 |
4.0233e-06 |
1.8328 |
0.086755511 |
0.2277418 |
| 250 |
CNOT8 |
5.58520e-06 |
3.0478e-06 |
1.8326 |
0.086792413 |
0.2277418 |
| 361 |
NSMCE3 |
4.40330e-06 |
2.4033e-06 |
1.8322 |
0.086847715 |
0.2277418 |
| 330 |
HEG1 |
2.81890e-06 |
1.5454e-06 |
1.8240 |
0.088140761 |
0.2277418 |
| 200 |
C18orf21 |
2.76400e-06 |
1.5156e-06 |
1.8237 |
0.088184171 |
0.2277418 |
| 71 |
RBM3 |
2.11160e-06 |
1.1580e-06 |
1.8234 |
0.088224910 |
0.2277418 |
| 303 |
SEC11C |
3.93570e-06 |
2.1626e-06 |
1.8199 |
0.088788892 |
0.2277418 |
| 371 |
IARS |
2.80550e-06 |
1.5460e-06 |
1.8147 |
0.089618225 |
0.2277418 |
| 210 |
CALM2 |
4.46570e-06 |
2.4631e-06 |
1.8130 |
0.089883328 |
0.2277418 |
| 422 |
RP11.5C23.1 |
3.40530e-06 |
1.8784e-06 |
1.8129 |
0.089912262 |
0.2277418 |
| 42 |
UBE2T |
6.17580e-06 |
3.4138e-06 |
1.8091 |
0.090518580 |
0.2279129 |
| 380 |
ZNF251 |
3.80510e-06 |
2.1203e-06 |
1.7946 |
0.092890807 |
0.2315996 |
| 133 |
EBPL |
2.84730e-06 |
1.5876e-06 |
1.7935 |
0.093077858 |
0.2315996 |
| 239 |
MED21 |
4.01810e-06 |
2.2543e-06 |
1.7824 |
0.094926764 |
0.2331687 |
| 17 |
ANAPC4 |
2.25540e-06 |
1.2657e-06 |
1.7820 |
0.095002997 |
0.2331687 |
| 117 |
BCAS2 |
2.83660e-06 |
1.5967e-06 |
1.7766 |
0.095921164 |
0.2331687 |
| 169 |
SRSF1 |
7.60040e-06 |
4.2973e-06 |
1.7686 |
0.097281687 |
0.2331687 |
| 196 |
DCAF5 |
3.62870e-06 |
2.0518e-06 |
1.7685 |
0.097295614 |
0.2331687 |
| 205 |
PFDN2 |
1.75540e-06 |
9.9700e-07 |
1.7606 |
0.098670037 |
0.2331687 |
| 352 |
HMGN4 |
2.40660e-06 |
1.3683e-06 |
1.7588 |
0.098990464 |
0.2331687 |
| 118 |
LGALS8 |
-2.02210e-06 |
1.1502e-06 |
-1.7580 |
0.099123799 |
0.2331687 |
| 206 |
POGZ |
2.30670e-06 |
1.3134e-06 |
1.7563 |
0.099421628 |
0.2331687 |
| 301 |
CUL5 |
2.55780e-06 |
1.4569e-06 |
1.7557 |
0.099540731 |
0.2331687 |
| 340 |
MEX3C |
4.68940e-06 |
2.6809e-06 |
1.7492 |
0.100680017 |
0.2331687 |
| 222 |
RNF44 |
4.25310e-06 |
2.4357e-06 |
1.7461 |
0.101225992 |
0.2331687 |
| 405 |
AC093818.1 |
-2.13550e-06 |
1.2237e-06 |
-1.7452 |
0.101396069 |
0.2331687 |
| 90 |
NAA25 |
2.08240e-06 |
1.1933e-06 |
1.7450 |
0.101425625 |
0.2331687 |
| 78 |
DECR1 |
4.27000e-06 |
2.4532e-06 |
1.7406 |
0.102221577 |
0.2332328 |
| 317 |
EMB |
3.08040e-06 |
1.7716e-06 |
1.7387 |
0.102556273 |
0.2332328 |
| 212 |
EAF1 |
6.27630e-06 |
3.6198e-06 |
1.7339 |
0.103441274 |
0.2333097 |
| 137 |
MED1 |
2.12890e-06 |
1.2288e-06 |
1.7325 |
0.103693216 |
0.2333097 |
| 376 |
TRIM33 |
3.22370e-06 |
1.8677e-06 |
1.7261 |
0.104864297 |
0.2337877 |
| 398 |
TRIM59 |
2.50090e-06 |
1.4498e-06 |
1.7250 |
0.105066368 |
0.2337877 |
| 360 |
AP3M1 |
3.38730e-06 |
1.9667e-06 |
1.7223 |
0.105563698 |
0.2337877 |
| 140 |
SLC10A3 |
4.18740e-06 |
2.4544e-06 |
1.7061 |
0.108600395 |
0.2389931 |
| 248 |
PTPRN2 |
4.59840e-06 |
2.6989e-06 |
1.7038 |
0.109044126 |
0.2389931 |
| 12 |
NSUN2 |
5.19410e-06 |
3.0760e-06 |
1.6886 |
0.111974871 |
0.2418219 |
| 348 |
PRKRA |
3.44240e-06 |
2.0402e-06 |
1.6873 |
0.112224304 |
0.2418219 |
| 177 |
ADAM10 |
2.83980e-06 |
1.6898e-06 |
1.6806 |
0.113545975 |
0.2418219 |
| 26 |
TAF2 |
1.75630e-06 |
1.0461e-06 |
1.6789 |
0.113880603 |
0.2418219 |
| 249 |
SAMSN1 |
4.32780e-06 |
2.5837e-06 |
1.6750 |
0.114647752 |
0.2418219 |
| 331 |
STAT5B |
1.95790e-06 |
1.1711e-06 |
1.6718 |
0.115283963 |
0.2418219 |
| 395 |
TRIQK |
3.50970e-06 |
2.1003e-06 |
1.6711 |
0.115428677 |
0.2418219 |
| 387 |
FOXJ3 |
4.96330e-06 |
2.9708e-06 |
1.6707 |
0.115503445 |
0.2418219 |
| 92 |
CLEC4A |
3.55190e-06 |
2.1285e-06 |
1.6688 |
0.115896522 |
0.2418219 |
| 362 |
LRRC37B |
2.55610e-06 |
1.5324e-06 |
1.6680 |
0.116051663 |
0.2418219 |
| 111 |
NOL10 |
2.91470e-06 |
1.7512e-06 |
1.6644 |
0.116783059 |
0.2421531 |
| 236 |
BAG3 |
5.08620e-06 |
3.0723e-06 |
1.6555 |
0.118590878 |
0.2437394 |
| 176 |
BUD13 |
1.43590e-06 |
8.6840e-07 |
1.6534 |
0.119024851 |
0.2437394 |
| 278 |
EIF5A2 |
2.05800e-06 |
1.2457e-06 |
1.6522 |
0.119276723 |
0.2437394 |
| 37 |
TSG101 |
3.13600e-06 |
1.9072e-06 |
1.6443 |
0.120902234 |
0.2449844 |
| 88 |
GTF2H1 |
2.99150e-06 |
1.8218e-06 |
1.6420 |
0.121380654 |
0.2449844 |
| 390 |
CIPC |
4.06480e-06 |
2.4777e-06 |
1.6406 |
0.121681751 |
0.2449844 |
| 43 |
SLC25A43 |
3.40730e-06 |
2.0800e-06 |
1.6381 |
0.122202612 |
0.2449844 |
| 275 |
WDR26 |
3.11080e-06 |
1.9085e-06 |
1.6300 |
0.123925125 |
0.2462548 |
| 46 |
EPB41L2 |
2.71150e-06 |
1.6641e-06 |
1.6294 |
0.124039425 |
0.2462548 |
| 339 |
PLEKHF2 |
4.26450e-06 |
2.6244e-06 |
1.6249 |
0.124995556 |
0.2462548 |
| 9 |
TBPL1 |
3.11940e-06 |
1.9206e-06 |
1.6242 |
0.125164974 |
0.2462548 |
| 269 |
EFCAB14 |
2.98850e-06 |
1.8530e-06 |
1.6128 |
0.127631633 |
0.2491234 |
| 191 |
TDG |
2.58600e-06 |
1.6076e-06 |
1.6086 |
0.128547284 |
0.2491234 |
| 171 |
HS6ST1 |
4.42760e-06 |
2.7564e-06 |
1.6063 |
0.129054179 |
0.2491234 |
| 23 |
GLTSCR1 |
3.37770e-06 |
2.1050e-06 |
1.6046 |
0.129430116 |
0.2491234 |
| 300 |
CCT2 |
3.25670e-06 |
2.0304e-06 |
1.6040 |
0.129567729 |
0.2491234 |
| 73 |
UBFD1 |
2.39320e-06 |
1.4958e-06 |
1.5999 |
0.130457815 |
0.2496998 |
| 102 |
ARL6 |
2.44470e-06 |
1.5449e-06 |
1.5824 |
0.134406297 |
0.2526953 |
| 49 |
AK6 |
4.02520e-06 |
2.5448e-06 |
1.5817 |
0.134565504 |
0.2526953 |
| 377 |
S100A10 |
3.44730e-06 |
2.1808e-06 |
1.5807 |
0.134793224 |
0.2526953 |
| 44 |
UBE2A |
4.47820e-06 |
2.8346e-06 |
1.5798 |
0.134995916 |
0.2526953 |
| 100 |
CCNG1 |
4.48800e-06 |
2.8419e-06 |
1.5792 |
0.135137621 |
0.2526953 |
| 353 |
X15.Sep |
4.56290e-06 |
2.8931e-06 |
1.5772 |
0.135607185 |
0.2526953 |
| 197 |
NCOA2 |
3.47770e-06 |
2.2205e-06 |
1.5662 |
0.138154347 |
0.2563127 |
| 238 |
ZFP36L2 |
4.37900e-06 |
2.8049e-06 |
1.5612 |
0.139318640 |
0.2573440 |
| 63 |
RPS6KA5 |
2.22400e-06 |
1.4408e-06 |
1.5436 |
0.143524983 |
0.2637747 |
| 56 |
NECAP1 |
5.04130e-06 |
3.2706e-06 |
1.5414 |
0.144047150 |
0.2637747 |
| 423 |
PIP4K2B |
1.58300e-06 |
1.0304e-06 |
1.5362 |
0.145302017 |
0.2649257 |
| 157 |
TSPAN2 |
2.60440e-06 |
1.7006e-06 |
1.5314 |
0.146474241 |
0.2659168 |
| 401 |
PPP1CB |
3.03230e-06 |
1.9932e-06 |
1.5213 |
0.148978935 |
0.2693081 |
| 229 |
LIN7C |
3.95340e-06 |
2.6056e-06 |
1.5173 |
0.149979350 |
0.2699628 |
| 125 |
UFM1 |
1.63190e-06 |
1.0788e-06 |
1.5127 |
0.151129514 |
0.2708804 |
| 397 |
HLA.A |
2.59910e-06 |
1.7216e-06 |
1.5097 |
0.151891337 |
0.2710972 |
| 298 |
GHITM |
2.25030e-06 |
1.4981e-06 |
1.5021 |
0.153823675 |
0.2721962 |
| 224 |
ZNF92 |
3.62740e-06 |
2.4172e-06 |
1.5007 |
0.154195422 |
0.2721962 |
| 36 |
AFF4 |
1.77720e-06 |
1.1859e-06 |
1.4986 |
0.154726933 |
0.2721962 |
| 25 |
ASUN |
2.06200e-06 |
1.3786e-06 |
1.4958 |
0.155459551 |
0.2721962 |
| 409 |
ARFGAP3 |
1.87170e-06 |
1.2537e-06 |
1.4929 |
0.156198309 |
0.2721962 |
| 164 |
DHX9 |
1.59860e-06 |
1.0713e-06 |
1.4922 |
0.156368026 |
0.2721962 |
| 62 |
TIMM9 |
2.07130e-06 |
1.3917e-06 |
1.4883 |
0.157395486 |
0.2728618 |
| 3 |
DYRK4 |
3.06070e-06 |
2.0704e-06 |
1.4783 |
0.160011685 |
0.2762651 |
| 170 |
NDUFB5 |
3.59890e-06 |
2.4512e-06 |
1.4682 |
0.162704516 |
0.2764408 |
| 302 |
TMX3 |
1.09570e-06 |
7.4650e-07 |
1.4678 |
0.162810886 |
0.2764408 |
| 7 |
DERA |
5.47730e-06 |
3.7479e-06 |
1.4614 |
0.164530978 |
0.2764408 |
| 231 |
PTS |
4.16260e-06 |
2.8493e-06 |
1.4609 |
0.164665948 |
0.2764408 |
| 39 |
LMAN1 |
1.55240e-06 |
1.0635e-06 |
1.4597 |
0.164996215 |
0.2764408 |
| 276 |
CGGBP1 |
1.80900e-06 |
1.2403e-06 |
1.4586 |
0.165299939 |
0.2764408 |
| 180 |
THUMPD2 |
3.28450e-06 |
2.2521e-06 |
1.4584 |
0.165338860 |
0.2764408 |
| 308 |
MLST8 |
2.19560e-06 |
1.5074e-06 |
1.4565 |
0.165855688 |
0.2764408 |
| 190 |
POC1B |
3.75130e-06 |
2.5772e-06 |
1.4556 |
0.166125063 |
0.2764408 |
| 113 |
SRSF7 |
3.48800e-06 |
2.3995e-06 |
1.4536 |
0.166648707 |
0.2764408 |
| 211 |
ACKR3 |
4.85660e-06 |
3.3514e-06 |
1.4491 |
0.167883244 |
0.2774008 |
| 29 |
NDUFB4 |
4.94960e-06 |
3.4267e-06 |
1.4444 |
0.169181834 |
0.2784588 |
| 1 |
LAMP2 |
2.88940e-06 |
2.0038e-06 |
1.4419 |
0.169875710 |
0.2785172 |
| 109 |
UNC50 |
3.17820e-06 |
2.2177e-06 |
1.4331 |
0.172337829 |
0.2814629 |
| 346 |
GRAMD1C |
1.63250e-06 |
1.1493e-06 |
1.4204 |
0.175947431 |
0.2856602 |
| 218 |
OCIAD2 |
4.39500e-06 |
3.0966e-06 |
1.4193 |
0.176258392 |
0.2856602 |
| 34 |
CDC42 |
2.79870e-06 |
1.9861e-06 |
1.4091 |
0.179194074 |
0.2870135 |
| 167 |
TBC1D4 |
2.65570e-06 |
1.8883e-06 |
1.4064 |
0.179986175 |
0.2870135 |
| 335 |
GCSAM |
-1.45850e-06 |
1.0376e-06 |
-1.4056 |
0.180217011 |
0.2870135 |
| 230 |
CPSF7 |
4.01630e-06 |
2.8621e-06 |
1.4033 |
0.180900632 |
0.2870135 |
| 108 |
WDR75 |
3.67760e-06 |
2.6208e-06 |
1.4032 |
0.180906647 |
0.2870135 |
| 18 |
TAB2 |
2.00410e-06 |
1.4296e-06 |
1.4018 |
0.181323520 |
0.2870135 |
| 147 |
TEP1 |
1.63760e-06 |
1.1716e-06 |
1.3978 |
0.182497373 |
0.2870135 |
| 281 |
RCHY1 |
3.95030e-06 |
2.8262e-06 |
1.3977 |
0.182521556 |
0.2870135 |
| 75 |
SGK3 |
-1.37900e-06 |
9.8840e-07 |
-1.3952 |
0.183260019 |
0.2871074 |
| 315 |
PDCD6IP |
2.56370e-06 |
1.8498e-06 |
1.3859 |
0.186034860 |
0.2903791 |
| 307 |
RP11.25K19.1 |
2.30330e-06 |
1.6652e-06 |
1.3832 |
0.186859745 |
0.2905944 |
| 410 |
CCDC71L |
3.85640e-06 |
2.7933e-06 |
1.3806 |
0.187623289 |
0.2907130 |
| 53 |
PGS1 |
2.37300e-06 |
1.7308e-06 |
1.3711 |
0.190521898 |
0.2941269 |
| 178 |
GTF2B |
2.21940e-06 |
1.6328e-06 |
1.3593 |
0.194145858 |
0.2986316 |
| 13 |
CLEC16A |
1.66550e-06 |
1.2314e-06 |
1.3526 |
0.196226200 |
0.2999954 |
| 415 |
INAFM2 |
4.53300e-06 |
3.3531e-06 |
1.3519 |
0.196450913 |
0.2999954 |
| 396 |
LIN52 |
1.29620e-06 |
9.6300e-07 |
1.3461 |
0.198262482 |
0.3016728 |
| 319 |
C1GALT1C1 |
1.64830e-06 |
1.2447e-06 |
1.3243 |
0.205243988 |
0.3111764 |
| 247 |
KLF10 |
4.89020e-06 |
3.7181e-06 |
1.3152 |
0.208182406 |
0.3145041 |
| 57 |
PUS7 |
2.21110e-06 |
1.6858e-06 |
1.3116 |
0.209370471 |
0.3151733 |
| 155 |
ARNTL |
2.20600e-06 |
1.6870e-06 |
1.3077 |
0.210666212 |
0.3153092 |
| 98 |
PAPD7 |
3.57400e-06 |
2.7349e-06 |
1.3068 |
0.210951553 |
0.3153092 |
| 389 |
PRMT6 |
3.05770e-06 |
2.3741e-06 |
1.2879 |
0.217282245 |
0.3236281 |
| 329 |
PARP15 |
2.78290e-06 |
2.1747e-06 |
1.2797 |
0.220094652 |
0.3266668 |
| 408 |
RP11.666F17.1 |
2.37370e-06 |
1.8624e-06 |
1.2746 |
0.221854017 |
0.3281267 |
| 310 |
PDHB |
1.67100e-06 |
1.3240e-06 |
1.2621 |
0.226182621 |
0.3333632 |
| 217 |
MANF |
3.43600e-06 |
2.7723e-06 |
1.2394 |
0.234251975 |
0.3440576 |
| 344 |
UBE2N |
2.86410e-06 |
2.3363e-06 |
1.2259 |
0.239128719 |
0.3500050 |
| 41 |
ARHGAP15 |
1.69160e-06 |
1.3845e-06 |
1.2218 |
0.240640372 |
0.3510030 |
| 50 |
SLC25A24 |
2.78980e-06 |
2.3062e-06 |
1.2097 |
0.245124759 |
0.3563154 |
| 163 |
RNASEL |
1.34790e-06 |
1.1185e-06 |
1.2051 |
0.246827220 |
0.3575379 |
| 14 |
YTHDC2 |
1.89060e-06 |
1.5717e-06 |
1.2029 |
0.247656249 |
0.3575379 |
| 45 |
TIGAR |
3.00730e-06 |
2.5058e-06 |
1.2001 |
0.248698551 |
0.3578214 |
| 286 |
ERAP1 |
1.44070e-06 |
1.2057e-06 |
1.1949 |
0.250670512 |
0.3594360 |
| 342 |
FAM91A1 |
2.83560e-06 |
2.4189e-06 |
1.1722 |
0.259384060 |
0.3702244 |
| 321 |
JMJD1C |
-1.10480e-06 |
9.4360e-07 |
-1.1708 |
0.259944799 |
0.3702244 |
| 35 |
RDH11 |
1.85660e-06 |
1.6008e-06 |
1.1599 |
0.264239072 |
0.3750776 |
| 304 |
NEMP1 |
2.20750e-06 |
1.9225e-06 |
1.1482 |
0.268849670 |
0.3803459 |
| 290 |
TP53INP1 |
2.07190e-06 |
1.8131e-06 |
1.1427 |
0.271070317 |
0.3822091 |
| 59 |
FKBP5 |
1.21310e-06 |
1.0682e-06 |
1.1357 |
0.273915763 |
0.3849381 |
| 312 |
FAM84B |
2.40810e-06 |
2.1436e-06 |
1.1233 |
0.278948535 |
0.3907127 |
| 355 |
TMEM50A |
1.05420e-06 |
9.4400e-07 |
1.1167 |
0.281694800 |
0.3932571 |
| 386 |
PNP |
2.52290e-06 |
2.2800e-06 |
1.1065 |
0.285926965 |
0.3978523 |
| 412 |
TRAPPC2B |
1.80360e-06 |
1.6344e-06 |
1.1035 |
0.287195687 |
0.3983075 |
| 179 |
RABGGTB |
-1.07500e-06 |
9.7800e-07 |
-1.0992 |
0.289007125 |
0.3983943 |
| 122 |
ALG2 |
1.94160e-06 |
1.7669e-06 |
1.0989 |
0.289141966 |
0.3983943 |
| 337 |
ZNF654 |
1.15670e-06 |
1.0566e-06 |
1.0947 |
0.290895239 |
0.3995087 |
| 343 |
ZDHHC13 |
1.56840e-06 |
1.4359e-06 |
1.0923 |
0.291941393 |
0.3996479 |
| 52 |
TMED2 |
2.63390e-06 |
2.4228e-06 |
1.0871 |
0.294151264 |
0.4001288 |
| 263 |
TAB3 |
1.19310e-06 |
1.0976e-06 |
1.0870 |
0.294184530 |
0.4001288 |
| 91 |
GOLT1B |
2.48020e-06 |
2.3227e-06 |
1.0678 |
0.302491398 |
0.4099161 |
| 172 |
FAM8A1 |
2.19760e-06 |
2.0617e-06 |
1.0659 |
0.303318569 |
0.4099161 |
| 280 |
CD200R1 |
2.03470e-06 |
1.9158e-06 |
1.0621 |
0.305003377 |
0.4108803 |
| 349 |
SIAH2 |
3.04190e-06 |
2.8714e-06 |
1.0594 |
0.306177516 |
0.4111527 |
| 61 |
ASCC2 |
1.24790e-06 |
1.1824e-06 |
1.0554 |
0.307945913 |
0.4122187 |
| 128 |
TMPO |
2.01320e-06 |
1.9264e-06 |
1.0451 |
0.312546743 |
0.4170576 |
| 265 |
PPP1R15B |
-9.63600e-07 |
9.3060e-07 |
-1.0355 |
0.316857814 |
0.4214807 |
| 243 |
NUS1 |
2.52400e-06 |
2.4770e-06 |
1.0190 |
0.324370341 |
0.4290081 |
| 153 |
KIAA0907 |
1.53040e-06 |
1.5025e-06 |
1.0186 |
0.324545108 |
0.4290081 |
| 326 |
HPSE |
1.62180e-06 |
1.6033e-06 |
1.0115 |
0.327802856 |
0.4319645 |
| 150 |
VIMP |
1.59470e-06 |
1.5866e-06 |
1.0051 |
0.330788227 |
0.4345448 |
| 67 |
PRELID3B |
2.41230e-06 |
2.4245e-06 |
0.9950 |
0.335519188 |
0.4393951 |
| 383 |
TXNRD1 |
1.22950e-06 |
1.2613e-06 |
0.9748 |
0.345115688 |
0.4494189 |
| 120 |
PLAGL1 |
1.59590e-06 |
1.6378e-06 |
0.9744 |
0.345298222 |
0.4494189 |
| 368 |
CERKL |
2.32480e-06 |
2.4042e-06 |
0.9670 |
0.348877787 |
0.4526850 |
| 254 |
FAM161B |
1.10630e-06 |
1.1586e-06 |
0.9549 |
0.354762226 |
0.4589126 |
| 246 |
ATP5J |
1.51480e-06 |
1.6082e-06 |
0.9419 |
0.361167328 |
0.4657737 |
| 168 |
ITM2B |
1.41630e-06 |
1.5263e-06 |
0.9279 |
0.368153491 |
0.4724136 |
| 357 |
SH2D1A |
2.33770e-06 |
2.5215e-06 |
0.9271 |
0.368549633 |
0.4724136 |
| 228 |
NOTCH1 |
1.96880e-06 |
2.1395e-06 |
0.9202 |
0.372030706 |
0.4740088 |
| 76 |
ZDHHC2 |
2.40420e-06 |
2.6127e-06 |
0.9202 |
0.372035260 |
0.4740088 |
| 72 |
FNDC3A |
-7.58700e-07 |
8.2700e-07 |
-0.9175 |
0.373414653 |
0.4743375 |
| 354 |
HMCES |
1.04770e-06 |
1.1514e-06 |
0.9100 |
0.377220979 |
0.4777379 |
| 258 |
MFSD14A |
1.94500e-06 |
2.1432e-06 |
0.9075 |
0.378495518 |
0.4779212 |
| 350 |
FAM89A |
1.45810e-06 |
1.6280e-06 |
0.8956 |
0.384608672 |
0.4841948 |
| 375 |
MAFG |
3.12940e-06 |
3.5275e-06 |
0.8871 |
0.389004020 |
0.4882751 |
| 311 |
CMAHP |
1.86040e-06 |
2.1299e-06 |
0.8735 |
0.396166981 |
0.4957948 |
| 173 |
CPEB2 |
1.92080e-06 |
2.2072e-06 |
0.8703 |
0.397872751 |
0.4964607 |
| 183 |
SPPL2A |
7.48100e-07 |
8.6600e-07 |
0.8639 |
0.401261530 |
0.4992166 |
| 309 |
MAPK1IP1L |
-1.17290e-06 |
1.3696e-06 |
-0.8564 |
0.405241713 |
0.5026899 |
| 70 |
METTL4 |
9.44600e-07 |
1.1081e-06 |
0.8524 |
0.407400939 |
0.5038906 |
| 347 |
MAF |
-1.01330e-06 |
1.1932e-06 |
-0.8492 |
0.409121506 |
0.5045434 |
| 379 |
IRAK4 |
1.06720e-06 |
1.2625e-06 |
0.8453 |
0.411236212 |
0.5056771 |
| 16 |
MSMO1 |
2.35500e-06 |
2.8228e-06 |
0.8343 |
0.417200020 |
0.5115235 |
| 112 |
RAB3GAP1 |
3.75300e-07 |
4.5340e-07 |
0.8276 |
0.420854958 |
0.5145134 |
| 83 |
RHEB |
1.96610e-06 |
2.4022e-06 |
0.8185 |
0.425905475 |
0.5191874 |
| 139 |
FAM78A |
-1.41850e-06 |
1.7598e-06 |
-0.8061 |
0.432794767 |
0.5260695 |
| 418 |
RP11.154H23.3 |
1.13640e-06 |
1.4175e-06 |
0.8017 |
0.435223151 |
0.5275054 |
| 417 |
NBPF12 |
1.09770e-06 |
1.3848e-06 |
0.7927 |
0.440311028 |
0.5321473 |
| 182 |
EXOC6 |
9.33000e-07 |
1.1902e-06 |
0.7839 |
0.445280317 |
0.5366199 |
| 264 |
SLC37A3 |
1.74150e-06 |
2.2312e-06 |
0.7805 |
0.447231193 |
0.5374398 |
| 77 |
NBN |
9.03700e-07 |
1.1681e-06 |
0.7737 |
0.451151170 |
0.5406146 |
| 48 |
CHMP2B |
1.59320e-06 |
2.1009e-06 |
0.7583 |
0.460007192 |
0.5496696 |
| 126 |
ELF1 |
-5.36500e-07 |
7.1280e-07 |
-0.7528 |
0.463240730 |
0.5519742 |
| 394 |
SYT15 |
-1.12130e-06 |
1.5046e-06 |
-0.7453 |
0.467632040 |
0.5556414 |
| 414 |
CTD.2501E16.2 |
1.22470e-06 |
1.6546e-06 |
0.7402 |
0.470610346 |
0.5576139 |
| 271 |
SLC37A1 |
1.37450e-06 |
1.8652e-06 |
0.7369 |
0.472539336 |
0.5583356 |
| 166 |
SCYL2 |
7.52200e-07 |
1.0533e-06 |
0.7141 |
0.486120592 |
0.5727828 |
| 114 |
TIA1 |
5.62400e-07 |
8.0220e-07 |
0.7011 |
0.493976523 |
0.5790126 |
| 192 |
NUP58 |
-4.98900e-07 |
7.1190e-07 |
-0.7008 |
0.494145466 |
0.5790126 |
| 32 |
FTSJ1 |
-8.74100e-07 |
1.3350e-06 |
-0.6547 |
0.522549850 |
0.6106038 |
| 223 |
PRIM2 |
1.08070e-06 |
1.6864e-06 |
0.6408 |
0.531291748 |
0.6180032 |
| 324 |
OXSR1 |
1.03510e-06 |
1.6173e-06 |
0.6400 |
0.531804200 |
0.6180032 |
| 6 |
MDH1 |
1.40240e-06 |
2.3887e-06 |
0.5871 |
0.565873727 |
0.6546316 |
| 174 |
FCHSD2 |
6.83000e-07 |
1.1650e-06 |
0.5863 |
0.566418799 |
0.6546316 |
| 213 |
CSRNP1 |
-1.28150e-06 |
2.2096e-06 |
-0.5800 |
0.570547034 |
0.6566089 |
| 242 |
CEBPG |
-5.07000e-07 |
8.7570e-07 |
-0.5789 |
0.571234188 |
0.6566089 |
| 294 |
REEP3 |
6.80800e-07 |
1.1832e-06 |
0.5754 |
0.573566461 |
0.6567126 |
| 135 |
RAP2C |
1.11050e-06 |
1.9345e-06 |
0.5741 |
0.574429481 |
0.6567126 |
| 273 |
SLC30A7 |
7.22500e-07 |
1.2724e-06 |
0.5678 |
0.578577016 |
0.6596714 |
| 411 |
IFNG.AS1 |
-8.24800e-07 |
1.5321e-06 |
-0.5383 |
0.598237610 |
0.6798211 |
| 235 |
PARP8 |
-5.16700e-07 |
9.6310e-07 |
-0.5365 |
0.599463980 |
0.6798211 |
| 287 |
ACSL6 |
6.71200e-07 |
1.2757e-06 |
0.5262 |
0.606457183 |
0.6859128 |
| 66 |
GINS1 |
7.31500e-07 |
1.3973e-06 |
0.5235 |
0.608282013 |
0.6861421 |
| 257 |
EEF1A1 |
-1.42030e-06 |
2.7998e-06 |
-0.5073 |
0.619314404 |
0.6967287 |
| 413 |
KIAA1147 |
6.69900e-07 |
1.3276e-06 |
0.5046 |
0.621139124 |
0.6969280 |
| 358 |
VPS33B |
5.70900e-07 |
1.1391e-06 |
0.5012 |
0.623514666 |
0.6977426 |
| 201 |
MBD1 |
7.87800e-07 |
1.6014e-06 |
0.4919 |
0.629876300 |
0.7030018 |
| 27 |
SNX24 |
-5.35200e-07 |
1.1159e-06 |
-0.4796 |
0.638409472 |
0.7106505 |
| 334 |
TLR1 |
7.23100e-07 |
1.5551e-06 |
0.4650 |
0.648623574 |
0.7176970 |
| 393 |
NAGA |
-4.90400e-07 |
1.0562e-06 |
-0.4643 |
0.649080019 |
0.7176970 |
| 11 |
UBA6 |
-4.46300e-07 |
9.6330e-07 |
-0.4633 |
0.649829658 |
0.7176970 |
| 208 |
EFNA3 |
8.02200e-07 |
1.7586e-06 |
0.4561 |
0.654824480 |
0.7213301 |
| 134 |
AMD1 |
-5.35300e-07 |
1.1855e-06 |
-0.4516 |
0.658032413 |
0.7229811 |
| 33 |
CLEC2D |
7.10000e-07 |
1.5964e-06 |
0.4447 |
0.662856197 |
0.7263942 |
| 385 |
TTC37 |
3.76900e-07 |
8.5440e-07 |
0.4411 |
0.665439455 |
0.7273408 |
| 85 |
TLE4 |
4.52400e-07 |
1.0453e-06 |
0.4328 |
0.671317164 |
0.7318741 |
| 161 |
BICDL1 |
-7.45200e-07 |
1.7348e-06 |
-0.4295 |
0.673632389 |
0.7319654 |
| 328 |
LRRN3 |
-8.84800e-07 |
2.0682e-06 |
-0.4278 |
0.674861755 |
0.7319654 |
| 382 |
GFPT1 |
4.14400e-07 |
1.0089e-06 |
0.4108 |
0.687020650 |
0.7429051 |
| 356 |
TBK1 |
-3.63500e-07 |
8.8920e-07 |
-0.4088 |
0.688460477 |
0.7429051 |
| 104 |
EPB41L5 |
6.98300e-07 |
1.7204e-06 |
0.4059 |
0.690571913 |
0.7432873 |
| 388 |
SFMBT2 |
6.38600e-07 |
1.5893e-06 |
0.4018 |
0.693481055 |
0.7445241 |
| 132 |
SPATA1 |
6.67700e-07 |
1.7325e-06 |
0.3854 |
0.705365758 |
0.7553664 |
| 40 |
MYDGF |
1.69130e-06 |
4.5079e-06 |
0.3752 |
0.712771399 |
0.7613694 |
| 259 |
SEC13 |
-6.57700e-07 |
1.7809e-06 |
-0.3693 |
0.717055964 |
0.7640168 |
| 82 |
TWISTNB |
4.33100e-07 |
1.1850e-06 |
0.3655 |
0.719874545 |
0.7650928 |
| 237 |
UHMK1 |
4.32600e-07 |
1.2471e-06 |
0.3469 |
0.733498249 |
0.7776184 |
| 372 |
CTBP1.AS2 |
3.93800e-07 |
1.1626e-06 |
0.3387 |
0.739501628 |
0.7809241 |
| 86 |
MAP3K8 |
4.56900e-07 |
1.3576e-06 |
0.3365 |
0.741134221 |
0.7809241 |
| 419 |
NBPF19 |
3.95200e-07 |
1.1792e-06 |
0.3351 |
0.742154803 |
0.7809241 |
| 384 |
BAZ1A |
-4.53200e-07 |
1.3795e-06 |
-0.3286 |
0.747036984 |
0.7841108 |
| 255 |
DCK |
4.74800e-07 |
1.4663e-06 |
0.3238 |
0.750544387 |
0.7858423 |
| 215 |
NFKBIZ |
-6.38600e-07 |
2.2198e-06 |
-0.2877 |
0.777514307 |
0.8120705 |
| 233 |
KIN |
-2.01500e-07 |
7.2780e-07 |
-0.2769 |
0.785639001 |
0.8185352 |
| 154 |
USPL1 |
3.47900e-07 |
1.3003e-06 |
0.2675 |
0.792718681 |
0.8238821 |
| 131 |
KHDRBS1 |
2.29900e-07 |
8.9040e-07 |
0.2582 |
0.799739716 |
0.8291419 |
| 373 |
PPTC7 |
3.60900e-07 |
1.4152e-06 |
0.2550 |
0.802158380 |
0.8296161 |
| 80 |
OAZ1 |
2.34000e-07 |
9.6000e-07 |
0.2438 |
0.810695386 |
0.8364004 |
| 266 |
ELK4 |
1.91800e-07 |
8.6710e-07 |
0.2212 |
0.827929089 |
0.8521022 |
| 95 |
E2F3 |
-2.88400e-07 |
1.5608e-06 |
-0.1848 |
0.855897051 |
0.8787487 |
| 320 |
SPSB1 |
-2.15200e-07 |
1.3364e-06 |
-0.1611 |
0.874195150 |
0.8939597 |
| 186 |
CNOT6L |
-1.30800e-07 |
8.1720e-07 |
-0.1601 |
0.874939287 |
0.8939597 |
| 219 |
NAF1 |
1.53700e-07 |
1.1579e-06 |
0.1328 |
0.896127932 |
0.9134027 |
| 65 |
PCIF1 |
-1.64400e-07 |
1.5256e-06 |
-0.1078 |
0.915594410 |
0.9310010 |
| 288 |
CREBRF |
9.08000e-08 |
8.6700e-07 |
0.1047 |
0.917968802 |
0.9311770 |
| 5 |
ZC3H3 |
-7.78000e-08 |
1.4195e-06 |
-0.0548 |
0.957021257 |
0.9684689 |
| 336 |
GPR171 |
6.20000e-08 |
1.6431e-06 |
0.0377 |
0.970390054 |
0.9773498 |
| 295 |
MICU2 |
3.21000e-08 |
8.5110e-07 |
0.0377 |
0.970418277 |
0.9773498 |
| 162 |
CCDC146 |
-4.60000e-08 |
1.4513e-06 |
-0.0317 |
0.975145805 |
0.9797783 |
| 93 |
C2CD5 |
3.64000e-08 |
1.3149e-06 |
0.0277 |
0.978264119 |
0.9805823 |
| 22 |
ELMO2 |
-1.03000e-08 |
8.8670e-07 |
-0.0116 |
0.990910940 |
0.9909109 |
isgs.rld.lin[, 235] == genesbeta.rld.lin[, 428]
## [1] NA NA NA NA NA NA NA NA NA NA NA NA NA TRUE
## [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [29] TRUE TRUE TRUE TRUE
################# CD4 Counts ################# whole isgs
gene_FunReg(as.matrix(isgs.rld.lin[, 2:231]), isgs.rld.lin[,
234], "Core ISGs", "CD4 Counts")
Top Genes from Core ISGs Associated with Outcome: CD4 Counts by p.value (Sample Size = -18801)
| 172 |
IRS1 |
0.0007610715 |
0.0001482952 |
5.1321 |
1.932496e-05 |
0.004444741 |
| 126 |
MVB12A |
-0.0010835714 |
0.0002476611 |
-4.3752 |
1.525605e-04 |
0.017544461 |
| 187 |
ODF3B |
-0.0015686938 |
0.0004039165 |
-3.8837 |
5.734632e-04 |
0.029788242 |
| 45 |
LGALS3BP |
-0.0007490935 |
0.0001939187 |
-3.8629 |
6.061176e-04 |
0.029788242 |
| 190 |
UBA7 |
-0.0010256825 |
0.0002672392 |
-3.8381 |
6.475705e-04 |
0.029788242 |
| 181 |
MYD88 |
0.0012700210 |
0.0003375633 |
3.7623 |
7.917648e-04 |
0.030350986 |
| 20 |
LAG3 |
-0.0022022688 |
0.0006142794 |
-3.5851 |
1.262499e-03 |
0.041351330 |
| 214 |
ASAH2B |
0.0014553747 |
0.0004129725 |
3.5241 |
1.480444e-03 |
0.041351330 |
| 203 |
TDRD7 |
0.0017143951 |
0.0004915349 |
3.4878 |
1.627094e-03 |
0.041351330 |
| 220 |
AC009950.2 |
-0.0018182819 |
0.0005287117 |
-3.4391 |
1.846379e-03 |
0.041351330 |
| 38 |
C1GALT1 |
0.0006697419 |
0.0001962611 |
3.4125 |
1.977672e-03 |
0.041351330 |
| 145 |
MOV10 |
-0.0006626383 |
0.0001967015 |
-3.3688 |
2.213713e-03 |
0.042429506 |
| 47 |
UNC93B1 |
-0.0009141223 |
0.0002743428 |
-3.3320 |
2.432518e-03 |
0.043036866 |
| 224 |
PSMB9 |
-0.0017736404 |
0.0005453889 |
-3.2521 |
2.983743e-03 |
0.048429186 |
| 26 |
PSME2 |
-0.0011765994 |
0.0003643089 |
-3.2297 |
3.158425e-03 |
0.048429186 |
| 180 |
AFF1 |
0.0011163424 |
0.0003504499 |
3.1855 |
3.532698e-03 |
0.050782536 |
| 122 |
NLRC5 |
-0.0014858749 |
0.0004831703 |
-3.0753 |
4.659137e-03 |
0.061185867 |
| 183 |
CNP |
-0.0006228970 |
0.0002043938 |
-3.0475 |
4.992483e-03 |
0.061185867 |
| 198 |
TRIM69 |
-0.0010965476 |
0.0003655343 |
-2.9998 |
5.619499e-03 |
0.061185867 |
| 65 |
BLZF1 |
0.0004353983 |
0.0001454242 |
2.9940 |
5.701552e-03 |
0.061185867 |
| 37 |
PRKD2 |
-0.0007526942 |
0.0002529494 |
-2.9757 |
5.965341e-03 |
0.061185867 |
| 53 |
CCND3 |
-0.0006605088 |
0.0002224638 |
-2.9691 |
6.063350e-03 |
0.061185867 |
| 211 |
TMEM229B |
-0.0011605751 |
0.0003957111 |
-2.9329 |
6.627422e-03 |
0.061185867 |
| 228 |
RP3.508I15.21 |
-0.0010991850 |
0.0003755405 |
-2.9269 |
6.724723e-03 |
0.061185867 |
| 200 |
ISG15 |
-0.0022389112 |
0.0007678216 |
-2.9159 |
6.908636e-03 |
0.061185867 |
| 34 |
PARP4 |
0.0004448793 |
0.0001542342 |
2.8844 |
7.460929e-03 |
0.061185867 |
| 17 |
DNAJA1 |
0.0005798897 |
0.0002015356 |
2.8774 |
7.590822e-03 |
0.061185867 |
| 105 |
CHST12 |
-0.0007499669 |
0.0002607437 |
-2.8763 |
7.611105e-03 |
0.061185867 |
| 144 |
USP25 |
0.0004981413 |
0.0001735259 |
2.8707 |
7.714740e-03 |
0.061185867 |
| 222 |
TRIM26 |
-0.0007458627 |
0.0002620257 |
-2.8465 |
8.181397e-03 |
0.062724044 |
| 58 |
GCA |
0.0007218355 |
0.0002567134 |
2.8118 |
8.897597e-03 |
0.066014432 |
| 157 |
CTSS |
-0.0005079175 |
0.0001830009 |
-2.7755 |
9.710942e-03 |
0.067890427 |
| 99 |
TRAFD1 |
0.0008270641 |
0.0002981757 |
2.7737 |
9.751691e-03 |
0.067890427 |
| 5 |
SLC38A5 |
-0.0009863791 |
0.0003573311 |
-2.7604 |
1.006865e-02 |
0.067890427 |
| 18 |
CHMP5 |
0.0013876928 |
0.0005075771 |
2.7340 |
1.072590e-02 |
0.067890427 |
| 129 |
SLC18B1 |
-0.0003059680 |
0.0001120516 |
-2.7306 |
1.081211e-02 |
0.067890427 |
| 6 |
TYMP |
-0.0018290393 |
0.0006708685 |
-2.7264 |
1.092150e-02 |
0.067890427 |
| 107 |
TANK |
0.0004418309 |
0.0001637848 |
2.6976 |
1.169407e-02 |
0.070779925 |
| 174 |
TRIM56 |
-0.0006656211 |
0.0002493138 |
-2.6698 |
1.249017e-02 |
0.073039913 |
| 31 |
MYL12A |
0.0008372688 |
0.0003144472 |
2.6627 |
1.270259e-02 |
0.073039913 |
| 77 |
ZNFX1 |
-0.0011380574 |
0.0004322759 |
-2.6327 |
1.363073e-02 |
0.074283093 |
| 171 |
LGALS9 |
-0.0008269940 |
0.0003146165 |
-2.6286 |
1.376361e-02 |
0.074283093 |
| 93 |
ALOX5AP |
-0.0006109527 |
0.0002334813 |
-2.6167 |
1.415195e-02 |
0.074283093 |
| 84 |
SNX6 |
-0.0003112336 |
0.0001190212 |
-2.6149 |
1.421068e-02 |
0.074283093 |
| 188 |
PARP10 |
-0.0012017546 |
0.0004682792 |
-2.5663 |
1.591682e-02 |
0.081350628 |
| 163 |
DTX3L |
-0.0007715865 |
0.0003028539 |
-2.5477 |
1.661839e-02 |
0.081350628 |
| 175 |
STAT2 |
-0.0007711986 |
0.0003029924 |
-2.5453 |
1.671270e-02 |
0.081350628 |
| 194 |
IFITM2 |
-0.0011643989 |
0.0004587001 |
-2.5385 |
1.697752e-02 |
0.081350628 |
| 11 |
TBC1D1 |
-0.0002869006 |
0.0001141313 |
-2.5138 |
1.797272e-02 |
0.082687505 |
| 219 |
GBP1P1 |
-0.0019834924 |
0.0007890704 |
-2.5137 |
1.797554e-02 |
0.082687505 |
| 16 |
SP140 |
-0.0012043479 |
0.0004818170 |
-2.4996 |
1.856813e-02 |
0.082945231 |
| 42 |
SETX |
0.0003291428 |
0.0001319060 |
2.4953 |
1.875283e-02 |
0.082945231 |
| 25 |
APOL1 |
-0.0012276064 |
0.0004965735 |
-2.4722 |
1.977233e-02 |
0.085804453 |
| 130 |
DYNLT1 |
0.0012720611 |
0.0005230313 |
2.4321 |
2.165968e-02 |
0.091075581 |
| 226 |
RP11.468E2.4 |
-0.0012305421 |
0.0005064644 |
-2.4297 |
2.177894e-02 |
0.091075581 |
| 21 |
RGS1 |
0.0010924890 |
0.0004515582 |
2.4194 |
2.229256e-02 |
0.091283372 |
| 185 |
DRAP1 |
0.0004545708 |
0.0001888560 |
2.4070 |
2.292621e-02 |
0.091283372 |
| 217 |
IRF9 |
-0.0013114588 |
0.0005462964 |
-2.4006 |
2.325603e-02 |
0.091283372 |
| 7 |
TMSB10 |
0.0007495510 |
0.0003126268 |
2.3976 |
2.341617e-02 |
0.091283372 |
| 119 |
SCARB2 |
0.0006480421 |
0.0002729194 |
2.3745 |
2.466445e-02 |
0.093876717 |
| 92 |
XAF1 |
-0.0013356020 |
0.0005634782 |
-2.3703 |
2.489774e-02 |
0.093876717 |
| 100 |
CD164 |
0.0010169943 |
0.0004310393 |
2.3594 |
2.551152e-02 |
0.094639511 |
| 81 |
IFI6 |
-0.0020600915 |
0.0008773353 |
-2.3481 |
2.616220e-02 |
0.095512807 |
| 159 |
AZI2 |
0.0003076636 |
0.0001329935 |
2.3134 |
2.826334e-02 |
0.101571381 |
| 1 |
LAP3 |
-0.0008583774 |
0.0003728348 |
-2.3023 |
2.896444e-02 |
0.102489556 |
| 121 |
PML |
-0.0009161003 |
0.0004000079 |
-2.2902 |
2.974817e-02 |
0.103667853 |
| 140 |
GBP5 |
-0.0017522554 |
0.0007691946 |
-2.2780 |
3.055587e-02 |
0.104148350 |
| 127 |
IFITM3 |
-0.0013126885 |
0.0005792681 |
-2.2661 |
3.136666e-02 |
0.104148350 |
| 71 |
TRIM25 |
0.0006835689 |
0.0003022142 |
2.2619 |
3.166008e-02 |
0.104148350 |
| 170 |
TTC21A |
-0.0006297596 |
0.0002784904 |
-2.2613 |
3.169732e-02 |
0.104148350 |
| 109 |
STX17 |
-0.0002800037 |
0.0001271598 |
-2.2020 |
3.607044e-02 |
0.116847913 |
| 86 |
BST2 |
-0.0012477134 |
0.0005739157 |
-2.1740 |
3.831165e-02 |
0.122384428 |
| 196 |
ANKFY1 |
-0.0004304835 |
0.0001989244 |
-2.1641 |
3.914175e-02 |
0.123323316 |
| 128 |
MCL1 |
0.0006756275 |
0.0003161542 |
2.1370 |
4.147204e-02 |
0.128899578 |
| 13 |
IFI35 |
-0.0007241745 |
0.0003418864 |
-2.1182 |
4.316883e-02 |
0.130682655 |
| 184 |
RNF213 |
-0.0007705242 |
0.0003644015 |
-2.1145 |
4.350727e-02 |
0.130682655 |
| 59 |
STAT1 |
-0.0008216114 |
0.0003890452 |
-2.1119 |
4.375028e-02 |
0.130682655 |
| 182 |
PARP14 |
-0.0008285693 |
0.0003940227 |
-2.1028 |
4.459394e-02 |
0.131494963 |
| 147 |
MX1 |
-0.0016062367 |
0.0007677195 |
-2.0922 |
4.560670e-02 |
0.132778996 |
| 33 |
TNFSF13B |
-0.0008091647 |
0.0003901229 |
-2.0741 |
4.737746e-02 |
0.134859651 |
| 123 |
SECTM1 |
-0.0007527260 |
0.0003645223 |
-2.0650 |
4.829736e-02 |
0.134859651 |
| 28 |
SAMHD1 |
-0.0007488932 |
0.0003637907 |
-2.0586 |
4.894751e-02 |
0.134859651 |
| 22 |
PSME1 |
-0.0003503192 |
0.0001704750 |
-2.0550 |
4.932001e-02 |
0.134859651 |
| 164 |
YEATS2 |
0.0003398593 |
0.0001657758 |
2.0501 |
4.982209e-02 |
0.134859651 |
| 72 |
TNFSF10 |
-0.0006528738 |
0.0003184832 |
-2.0499 |
4.983944e-02 |
0.134859651 |
| 51 |
OAS2 |
-0.0013845240 |
0.0006792521 |
-2.0383 |
5.106444e-02 |
0.136567699 |
| 80 |
RBCK1 |
-0.0006773025 |
0.0003339869 |
-2.0279 |
5.217865e-02 |
0.137943569 |
| 63 |
GBP1 |
-0.0013166857 |
0.0006578202 |
-2.0016 |
5.510425e-02 |
0.144022465 |
| 158 |
GPR155 |
-0.0006551093 |
0.0003369670 |
-1.9441 |
6.198925e-02 |
0.158862169 |
| 61 |
FBXO6 |
-0.0007765893 |
0.0003997361 |
-1.9428 |
6.216346e-02 |
0.158862169 |
| 150 |
LY6E |
-0.0011344815 |
0.0005858161 |
-1.9366 |
6.294790e-02 |
0.159099076 |
| 56 |
FRMD4B |
0.0004272985 |
0.0002266786 |
1.8850 |
6.984181e-02 |
0.174604527 |
| 64 |
ECE1 |
-0.0004698165 |
0.0002520027 |
-1.8643 |
7.279076e-02 |
0.176809178 |
| 125 |
PMAIP1 |
0.0005020337 |
0.0002693866 |
1.8636 |
7.289425e-02 |
0.176809178 |
| 151 |
DBF4B |
-0.0006437485 |
0.0003467951 |
-1.8563 |
7.396595e-02 |
0.176809178 |
| 9 |
PARP12 |
-0.0003298893 |
0.0001782812 |
-1.8504 |
7.483626e-02 |
0.176809178 |
| 178 |
SNTB1 |
0.0005552807 |
0.0003003350 |
1.8489 |
7.506164e-02 |
0.176809178 |
| 27 |
REC8 |
-0.0006815416 |
0.0003695830 |
-1.8441 |
7.577723e-02 |
0.176809178 |
| 206 |
CASP4 |
-0.0004499502 |
0.0002448097 |
-1.8380 |
7.670086e-02 |
0.176809178 |
| 193 |
USP18 |
-0.0013205160 |
0.0007189137 |
-1.8368 |
7.687356e-02 |
0.176809178 |
| 2 |
CD38 |
-0.0008002076 |
0.0004381767 |
-1.8262 |
7.849846e-02 |
0.178639499 |
| 229 |
AC008079.10 |
-0.0010397941 |
0.0005708271 |
-1.8216 |
7.922273e-02 |
0.178639499 |
| 82 |
HELB |
-0.0006320468 |
0.0003479417 |
-1.8165 |
8.000962e-02 |
0.178662261 |
| 176 |
GIMAP8 |
-0.0004810982 |
0.0002656509 |
-1.8110 |
8.088049e-02 |
0.178870308 |
| 113 |
IFI44L |
-0.0017371281 |
0.0009961360 |
-1.7439 |
9.215368e-02 |
0.199999575 |
| 46 |
DHX58 |
-0.0005475066 |
0.0003143600 |
-1.7417 |
9.254652e-02 |
0.199999575 |
| 88 |
C19orf66 |
-0.0005726334 |
0.0003293135 |
-1.7389 |
9.304328e-02 |
0.199999575 |
| 101 |
USP15 |
0.0001939374 |
0.0001136891 |
1.7059 |
9.910531e-02 |
0.209784690 |
| 35 |
N4BP1 |
-0.0002020519 |
0.0001185616 |
-1.7042 |
9.941970e-02 |
0.209784690 |
| 4 |
NUB1 |
-0.0002879501 |
0.0001694957 |
-1.6989 |
1.004314e-01 |
0.209992984 |
| 201 |
FANCA |
-0.0004993951 |
0.0002967748 |
-1.6827 |
1.035454e-01 |
0.213324235 |
| 66 |
IFIT3 |
-0.0014041452 |
0.0008374730 |
-1.6766 |
1.047436e-01 |
0.213324235 |
| 155 |
GBP4 |
-0.0010553067 |
0.0006295364 |
-1.6763 |
1.048071e-01 |
0.213324235 |
| 132 |
STOM |
-0.0006184140 |
0.0003747379 |
-1.6503 |
1.100651e-01 |
0.222061169 |
| 166 |
IFI27 |
-0.0006615508 |
0.0004042347 |
-1.6366 |
1.129168e-01 |
0.225833525 |
| 97 |
CMPK2 |
-0.0009360359 |
0.0005795471 |
-1.6151 |
1.174995e-01 |
0.231518420 |
| 44 |
KPNB1 |
-0.0003212761 |
0.0001996016 |
-1.6096 |
1.187063e-01 |
0.231518420 |
| 136 |
GPR180 |
0.0003779430 |
0.0002352209 |
1.6068 |
1.193278e-01 |
0.231518420 |
| 117 |
HERC6 |
-0.0007946757 |
0.0004957958 |
-1.6028 |
1.201952e-01 |
0.231518420 |
| 177 |
PRKCE |
-0.0003554282 |
0.0002221235 |
-1.6001 |
1.207922e-01 |
0.231518420 |
| 73 |
ODF2L |
0.0002198147 |
0.0001391722 |
1.5794 |
1.254664e-01 |
0.238160344 |
| 111 |
DDX60 |
-0.0005266962 |
0.0003342625 |
-1.5757 |
1.263285e-01 |
0.238160344 |
| 161 |
AIM2 |
-0.0008317045 |
0.0005311319 |
-1.5659 |
1.286030e-01 |
0.240477124 |
| 24 |
JAK2 |
0.0002721690 |
0.0001795980 |
1.5154 |
1.408712e-01 |
0.261293379 |
| 76 |
NMI |
-0.0003771831 |
0.0002512363 |
-1.5013 |
1.444698e-01 |
0.265824377 |
| 52 |
TRIM38 |
-0.0002753587 |
0.0001842454 |
-1.4945 |
1.462249e-01 |
0.266918470 |
| 102 |
SP110 |
-0.0005008878 |
0.0003373691 |
-1.4847 |
1.487985e-01 |
0.269477550 |
| 36 |
EHD4 |
0.0003000116 |
0.0002031638 |
1.4767 |
1.509161e-01 |
0.271177359 |
| 23 |
NANS |
-0.0001880331 |
0.0001279356 |
-1.4697 |
1.527780e-01 |
0.272394828 |
| 104 |
SETDB2 |
0.0001644406 |
0.0001123929 |
1.4631 |
1.545795e-01 |
0.273469850 |
| 143 |
SLC25A28 |
0.0003617081 |
0.0002480193 |
1.4584 |
1.558610e-01 |
0.273469850 |
| 204 |
SPATS2L |
0.0001866083 |
0.0001283039 |
1.4544 |
1.569479e-01 |
0.273469850 |
| 218 |
APOL6 |
-0.0003971945 |
0.0002837236 |
-1.3999 |
1.725161e-01 |
0.298336038 |
| 213 |
RNY4P34 |
-0.0004467537 |
0.0003291947 |
-1.3571 |
1.855859e-01 |
0.318542919 |
| 48 |
MDK |
-0.0003322205 |
0.0002488517 |
-1.3350 |
1.926254e-01 |
0.328176662 |
| 230 |
RP11.640L9.2 |
-0.0002663434 |
0.0002008389 |
-1.3262 |
1.955054e-01 |
0.330634079 |
| 202 |
PLSCR1 |
0.0002772896 |
0.0002124856 |
1.3050 |
2.025228e-01 |
0.340001759 |
| 89 |
TRIM21 |
0.0002919197 |
0.0002277272 |
1.2819 |
2.103967e-01 |
0.350661168 |
| 74 |
NT5C3A |
0.0003403664 |
0.0002765914 |
1.2306 |
2.287201e-01 |
0.378457701 |
| 50 |
OAS3 |
-0.0007388047 |
0.0006031963 |
-1.2248 |
2.308491e-01 |
0.379252173 |
| 149 |
ADAR |
-0.0002123488 |
0.0001765533 |
-1.2027 |
2.391468e-01 |
0.387012071 |
| 191 |
MX2 |
-0.0007961528 |
0.0006619744 |
-1.2027 |
2.391665e-01 |
0.387012071 |
| 12 |
SP100 |
-0.0002806605 |
0.0002342943 |
-1.1979 |
2.409992e-01 |
0.387012071 |
| 62 |
GBP3 |
-0.0004182899 |
0.0003501798 |
-1.1945 |
2.423032e-01 |
0.387012071 |
| 114 |
IFI44 |
-0.0008705497 |
0.0007393347 |
-1.1775 |
2.489171e-01 |
0.394833983 |
| 40 |
TRIM14 |
-0.0001965567 |
0.0001707255 |
-1.1513 |
2.593445e-01 |
0.407330663 |
| 78 |
ZBP1 |
-0.0005711729 |
0.0004971689 |
-1.1489 |
2.603374e-01 |
0.407330663 |
| 154 |
NEXN |
-0.0002590988 |
0.0002279416 |
-1.1367 |
2.653031e-01 |
0.410676552 |
| 142 |
TTC39B |
-0.0002404309 |
0.0002118554 |
-1.1349 |
2.660470e-01 |
0.410676552 |
| 138 |
UTRN |
-0.0002160575 |
0.0001920908 |
-1.1248 |
2.702375e-01 |
0.414364159 |
| 210 |
CD2AP |
0.0001858361 |
0.0001683513 |
1.1039 |
2.790508e-01 |
0.421323216 |
| 153 |
RAVER2 |
0.0002913897 |
0.0002645854 |
1.1013 |
2.801406e-01 |
0.421323216 |
| 221 |
AC074338.4 |
0.0002976281 |
0.0002713651 |
1.0968 |
2.820806e-01 |
0.421323216 |
| 173 |
BUB1 |
0.0002610895 |
0.0002380622 |
1.0967 |
2.821034e-01 |
0.421323216 |
| 75 |
ACO1 |
-0.0001425985 |
0.0001305941 |
-1.0919 |
2.841743e-01 |
0.421677978 |
| 186 |
SAMD9L |
-0.0005163570 |
0.0004747990 |
-1.0875 |
2.860769e-01 |
0.421780044 |
| 223 |
APOBEC3G |
-0.0004163575 |
0.0003917897 |
-1.0627 |
2.969951e-01 |
0.432602404 |
| 146 |
UBE2L6 |
-0.0004551060 |
0.0004287841 |
-1.0614 |
2.975835e-01 |
0.432602404 |
| 32 |
FMR1 |
-0.0001436355 |
0.0001360826 |
-1.0555 |
3.002183e-01 |
0.432602404 |
| 3 |
ETV7 |
-0.0005754739 |
0.0005461695 |
-1.0537 |
3.010491e-01 |
0.432602404 |
| 55 |
XRN1 |
-0.0001860079 |
0.0001771970 |
-1.0497 |
3.028217e-01 |
0.432602404 |
| 43 |
LIPA |
0.0003754451 |
0.0003609755 |
1.0401 |
3.071989e-01 |
0.434000780 |
| 69 |
MASTL |
0.0001821137 |
0.0001752336 |
1.0393 |
3.075745e-01 |
0.434000780 |
| 156 |
CAPN2 |
0.0001705960 |
0.0001653477 |
1.0317 |
3.110236e-01 |
0.436191572 |
| 205 |
HSH2D |
-0.0002937619 |
0.0002927050 |
-1.0036 |
3.241611e-01 |
0.451860877 |
| 152 |
AK4 |
0.0001891084 |
0.0001907800 |
0.9912 |
3.300588e-01 |
0.457310356 |
| 49 |
PARP11 |
0.0001810996 |
0.0001946039 |
0.9306 |
3.600120e-01 |
0.495824849 |
| 10 |
TNK2 |
0.0001797142 |
0.0001949392 |
0.9219 |
3.644572e-01 |
0.496857220 |
| 95 |
C14orf159 |
0.0000939275 |
0.0001020196 |
0.9207 |
3.650820e-01 |
0.496857220 |
| 197 |
IFIT1 |
-0.0006999014 |
0.0007681111 |
-0.9112 |
3.699693e-01 |
0.500546740 |
| 195 |
IRF7 |
-0.0003838911 |
0.0004305019 |
-0.8917 |
3.801376e-01 |
0.509558766 |
| 216 |
SAMD9 |
-0.0002779836 |
0.0003126883 |
-0.8890 |
3.815710e-01 |
0.509558766 |
| 96 |
RSAD2 |
-0.0007050539 |
0.0007959634 |
-0.8858 |
3.832768e-01 |
0.509558766 |
| 167 |
SLFN5 |
-0.0004263116 |
0.0004879869 |
-0.8736 |
3.897604e-01 |
0.515200558 |
| 68 |
CD274 |
-0.0004819840 |
0.0005543755 |
-0.8694 |
3.920107e-01 |
0.515214095 |
| 137 |
IFIT5 |
0.0002542196 |
0.0003099705 |
0.8201 |
4.190629e-01 |
0.547639065 |
| 39 |
GIMAP2 |
0.0002951071 |
0.0003686242 |
0.8006 |
4.301251e-01 |
0.556513455 |
| 165 |
TLR3 |
0.0002572856 |
0.0003217812 |
0.7996 |
4.306930e-01 |
0.556513455 |
| 98 |
OASL |
-0.0003461253 |
0.0004436228 |
-0.7802 |
4.418050e-01 |
0.567682457 |
| 124 |
ZCCHC2 |
-0.0001293547 |
0.0001699393 |
-0.7612 |
4.529119e-01 |
0.578720706 |
| 103 |
PHF11 |
-0.0001167939 |
0.0001549250 |
-0.7539 |
4.572184e-01 |
0.580995775 |
| 192 |
RBM43 |
-0.0001380180 |
0.0001969051 |
-0.7009 |
4.891273e-01 |
0.618127847 |
| 91 |
TRIM22 |
-0.0003274848 |
0.0004712422 |
-0.6949 |
4.928203e-01 |
0.619391691 |
| 85 |
SAT1 |
-0.0001094232 |
0.0001586548 |
-0.6897 |
4.960640e-01 |
0.620079998 |
| 57 |
IFIH1 |
0.0002394268 |
0.0003525777 |
0.6791 |
5.026653e-01 |
0.624935233 |
| 108 |
CBWD2 |
0.0001306369 |
0.0002066798 |
0.6321 |
5.324661e-01 |
0.658425830 |
| 15 |
IPCEF1 |
-0.0001629183 |
0.0002647238 |
-0.6154 |
5.432429e-01 |
0.664563515 |
| 135 |
RASGRP3 |
0.0001561543 |
0.0002549821 |
0.6124 |
5.452065e-01 |
0.664563515 |
| 189 |
DDX60L |
-0.0002188625 |
0.0003581766 |
-0.6110 |
5.460978e-01 |
0.664563515 |
| 160 |
IFI16 |
0.0001802521 |
0.0003063049 |
0.5885 |
5.609325e-01 |
0.675895321 |
| 199 |
C11orf96 |
0.0002315298 |
0.0003938003 |
0.5879 |
5.612870e-01 |
0.675895321 |
| 179 |
ISG20 |
-0.0002050044 |
0.0003601742 |
-0.5692 |
5.737710e-01 |
0.687329900 |
| 131 |
TMEM140 |
-0.0001493054 |
0.0002769039 |
-0.5392 |
5.940136e-01 |
0.707891835 |
| 141 |
SLFN13 |
-0.0001798190 |
0.0003451547 |
-0.5210 |
6.064762e-01 |
0.719018197 |
| 116 |
PARP9 |
0.0002518720 |
0.0004979640 |
0.5058 |
6.169537e-01 |
0.726728785 |
| 67 |
IFIT2 |
-0.0002721925 |
0.0005417605 |
-0.5024 |
6.192993e-01 |
0.726728785 |
| 209 |
C5orf56 |
-0.0001604796 |
0.0003261495 |
-0.4920 |
6.265246e-01 |
0.731475407 |
| 30 |
SMCHD1 |
0.0000544629 |
0.0001118558 |
0.4869 |
6.301172e-01 |
0.731954308 |
| 83 |
APOL2 |
-0.0001970901 |
0.0004190840 |
-0.4703 |
6.417921e-01 |
0.741769743 |
| 148 |
ADPGK |
0.0001049760 |
0.0002315466 |
0.4534 |
6.537774e-01 |
0.751843954 |
| 118 |
HERC5 |
0.0001939221 |
0.0004681977 |
0.4142 |
6.818920e-01 |
0.780274402 |
| 134 |
SCLT1 |
-0.0000616191 |
0.0001584014 |
-0.3890 |
7.002143e-01 |
0.797273666 |
| 90 |
TRIM5 |
0.0000909090 |
0.0002569921 |
0.3537 |
7.261816e-01 |
0.822767336 |
| 8 |
EIF2AK2 |
0.0000777300 |
0.0002247737 |
0.3458 |
7.320671e-01 |
0.824457874 |
| 162 |
PPM1K |
-0.0000913271 |
0.0002669735 |
-0.3421 |
7.348429e-01 |
0.824457874 |
| 208 |
GTF2E2 |
0.0000360135 |
0.0001114558 |
0.3231 |
7.490057e-01 |
0.836268493 |
| 60 |
IL18R1 |
-0.0000709687 |
0.0002320564 |
-0.3058 |
7.620000e-01 |
0.840957032 |
| 70 |
KIAA1217 |
0.0000539773 |
0.0001765185 |
0.3058 |
7.620279e-01 |
0.840957032 |
| 115 |
PNPT1 |
-0.0000949803 |
0.0003135271 |
-0.3029 |
7.641740e-01 |
0.840957032 |
| 169 |
TRANK1 |
-0.0000858467 |
0.0002885286 |
-0.2975 |
7.682563e-01 |
0.841423568 |
| 29 |
LPIN2 |
-0.0000521516 |
0.0001844055 |
-0.2828 |
7.794033e-01 |
0.849351121 |
| 212 |
CARD11 |
0.0001267209 |
0.0004583383 |
0.2765 |
7.842109e-01 |
0.849351121 |
| 54 |
FAM46A |
-0.0000517620 |
0.0001893458 |
-0.2734 |
7.865730e-01 |
0.849351121 |
| 87 |
HELZ2 |
-0.0000820111 |
0.0003401001 |
-0.2411 |
8.112052e-01 |
0.870790097 |
| 94 |
EPSTI1 |
-0.0001027516 |
0.0004335831 |
-0.2370 |
8.143957e-01 |
0.870790097 |
| 225 |
RP11.81H14.2 |
0.0000694511 |
0.0002986219 |
0.2326 |
8.177855e-01 |
0.870790097 |
| 133 |
ENDOD1 |
0.0000436403 |
0.0002200146 |
0.1984 |
8.442028e-01 |
0.894777188 |
| 79 |
MT2A |
-0.0000871077 |
0.0004661015 |
-0.1869 |
8.530978e-01 |
0.900057297 |
| 112 |
CASP1 |
-0.0000608492 |
0.0003408820 |
-0.1785 |
8.596115e-01 |
0.902788372 |
| 215 |
CARD16 |
0.0000525331 |
0.0003170108 |
0.1657 |
8.695728e-01 |
0.907122960 |
| 227 |
CTD.2047H16.2 |
0.0000854897 |
0.0005242195 |
0.1631 |
8.716268e-01 |
0.907122960 |
| 110 |
CMTR1 |
-0.0000198796 |
0.0001552333 |
-0.1281 |
8.990149e-01 |
0.929151274 |
| 139 |
MCOLN2 |
0.0000500376 |
0.0003980920 |
0.1257 |
9.008728e-01 |
0.929151274 |
| 41 |
DDX58 |
-0.0000460855 |
0.0003999647 |
-0.1152 |
9.090900e-01 |
0.933440589 |
| 14 |
DAPP1 |
0.0000298705 |
0.0003724669 |
0.0802 |
9.366515e-01 |
0.957465936 |
| 120 |
BRCA2 |
-0.0000158849 |
0.0002427739 |
-0.0654 |
9.482958e-01 |
0.965079844 |
| 168 |
NOD2 |
-0.0000142652 |
0.0002693233 |
-0.0530 |
9.581344e-01 |
0.970796983 |
| 207 |
PGAP1 |
0.0000070111 |
0.0002446822 |
0.0287 |
9.773439e-01 |
0.981739434 |
| 19 |
OAS1 |
-0.0000096169 |
0.0003375169 |
-0.0285 |
9.774710e-01 |
0.981739434 |
| 106 |
RTP4 |
-0.0000018121 |
0.0003808971 |
-0.0048 |
9.962378e-01 |
0.996237768 |
## betas
gene_FunReg(as.matrix(genesbeta.rld.lin[, 2:424]), genesbeta.rld.lin[,
427], "IFN-beta Genes", "CD4 Counts")
Top Genes from IFN-beta Genes Associated with Outcome: CD4 Counts by p.value (Sample Size = -18801)
| 85 |
TLE4 |
0.0005509871 |
0.0001202219 |
4.5831 |
8.663944e-05 |
0.01523938 |
| 385 |
TTC37 |
0.0005358599 |
0.0001287513 |
4.1620 |
2.717791e-04 |
0.01523938 |
| 359 |
CSF1 |
0.0012696458 |
0.0003114021 |
4.0772 |
3.415301e-04 |
0.01523938 |
| 131 |
KHDRBS1 |
0.0005601869 |
0.0001381998 |
4.0535 |
3.640346e-04 |
0.01523938 |
| 49 |
AK6 |
0.0014059302 |
0.0003525805 |
3.9875 |
4.344734e-04 |
0.01523938 |
| 350 |
FAM89A |
0.0009533171 |
0.0002401430 |
3.9698 |
4.556344e-04 |
0.01523938 |
| 307 |
RP11.25K19.1 |
0.0008657358 |
0.0002211048 |
3.9155 |
5.268229e-04 |
0.01523938 |
| 12 |
NSUN2 |
0.0015618595 |
0.0004038578 |
3.8674 |
5.990158e-04 |
0.01523938 |
| 412 |
TRAPPC2B |
0.0008937526 |
0.0002337691 |
3.8232 |
6.736309e-04 |
0.01523938 |
| 323 |
MUS81 |
0.0014277403 |
0.0003748157 |
3.8092 |
6.992467e-04 |
0.01523938 |
| 395 |
TRIQK |
0.0011726172 |
0.0003082922 |
3.8036 |
7.096999e-04 |
0.01523938 |
| 244 |
TCEB1 |
0.0010812639 |
0.0002848620 |
3.7957 |
7.246280e-04 |
0.01523938 |
| 10 |
GRN |
-0.0007831818 |
0.0002065103 |
-3.7925 |
7.309762e-04 |
0.01523938 |
| 187 |
USO1 |
0.0006495708 |
0.0001721166 |
3.7740 |
7.676093e-04 |
0.01523938 |
| 108 |
WDR75 |
0.0012639237 |
0.0003357579 |
3.7644 |
7.874356e-04 |
0.01523938 |
| 332 |
HOXB2 |
0.0013944974 |
0.0003721015 |
3.7476 |
8.231656e-04 |
0.01523938 |
| 285 |
LSM6 |
0.0011365405 |
0.0003062908 |
3.7107 |
9.076464e-04 |
0.01523938 |
| 415 |
INAFM2 |
0.0017077905 |
0.0004622833 |
3.6943 |
9.477999e-04 |
0.01523938 |
| 149 |
ZNF227 |
0.0016888185 |
0.0004607800 |
3.6651 |
1.023375e-03 |
0.01523938 |
| 185 |
NUP54 |
0.0007504855 |
0.0002054745 |
3.6525 |
1.058087e-03 |
0.01523938 |
| 62 |
TIMM9 |
0.0007878312 |
0.0002158457 |
3.6500 |
1.064998e-03 |
0.01523938 |
| 381 |
UCKL1 |
0.0016633265 |
0.0004585912 |
3.6270 |
1.131153e-03 |
0.01523938 |
| 169 |
SRSF1 |
0.0020739328 |
0.0005791145 |
3.5812 |
1.275491e-03 |
0.01523938 |
| 268 |
UBR1 |
0.0009275473 |
0.0002595275 |
3.5740 |
1.299839e-03 |
0.01523938 |
| 196 |
DCAF5 |
0.0011141710 |
0.0003121599 |
3.5692 |
1.316097e-03 |
0.01523938 |
| 109 |
UNC50 |
0.0012140825 |
0.0003409622 |
3.5608 |
1.345580e-03 |
0.01523938 |
| 389 |
PRMT6 |
0.0011019953 |
0.0003098296 |
3.5568 |
1.359628e-03 |
0.01523938 |
| 338 |
EIF1AD |
0.0017723645 |
0.0004984594 |
3.5557 |
1.363517e-03 |
0.01523938 |
| 182 |
EXOC6 |
0.0005968732 |
0.0001678907 |
3.5551 |
1.365496e-03 |
0.01523938 |
| 164 |
DHX9 |
0.0006371057 |
0.0001795923 |
3.5475 |
1.392927e-03 |
0.01523938 |
| 347 |
MAF |
0.0006288920 |
0.0001774002 |
3.5450 |
1.401914e-03 |
0.01523938 |
| 293 |
GTF2A1 |
0.0015621043 |
0.0004424363 |
3.5307 |
1.455412e-03 |
0.01523938 |
| 251 |
FAM126B |
0.0016794616 |
0.0004804588 |
3.4955 |
1.594871e-03 |
0.01523938 |
| 19 |
HPF1 |
0.0014028773 |
0.0004018056 |
3.4914 |
1.611976e-03 |
0.01523938 |
| 14 |
YTHDC2 |
0.0007766616 |
0.0002229816 |
3.4831 |
1.647364e-03 |
0.01523938 |
| 96 |
SMAP1 |
0.0011067563 |
0.0003182918 |
3.4772 |
1.672792e-03 |
0.01523938 |
| 204 |
RFWD2 |
0.0011060594 |
0.0003184453 |
3.4733 |
1.689652e-03 |
0.01523938 |
| 101 |
C5orf15 |
0.0023466261 |
0.0006764048 |
3.4693 |
1.707490e-03 |
0.01523938 |
| 18 |
TAB2 |
0.0007931006 |
0.0002298693 |
3.4502 |
1.793870e-03 |
0.01523938 |
| 74 |
TMEM87A |
0.0015804243 |
0.0004587707 |
3.4449 |
1.818721e-03 |
0.01523938 |
| 141 |
SHFM1 |
0.0015444091 |
0.0004490664 |
3.4392 |
1.846019e-03 |
0.01523938 |
| 209 |
SRP9 |
0.0018337032 |
0.0005342287 |
3.4324 |
1.878414e-03 |
0.01523938 |
| 410 |
CCDC71L |
0.0012392697 |
0.0003616280 |
3.4269 |
1.905381e-03 |
0.01523938 |
| 211 |
ACKR3 |
0.0016209200 |
0.0004732109 |
3.4254 |
1.913048e-03 |
0.01523938 |
| 125 |
UFM1 |
0.0005521568 |
0.0001612035 |
3.4252 |
1.913785e-03 |
0.01523938 |
| 36 |
AFF4 |
0.0006706892 |
0.0001960334 |
3.4213 |
1.933250e-03 |
0.01523938 |
| 333 |
C16orf91 |
0.0017175196 |
0.0005027810 |
3.4160 |
1.959702e-03 |
0.01523938 |
| 156 |
EMC7 |
0.0013912402 |
0.0004078755 |
3.4109 |
1.985660e-03 |
0.01523938 |
| 137 |
MED1 |
0.0005996231 |
0.0001758581 |
3.4097 |
1.992051e-03 |
0.01523938 |
| 327 |
TRMT112 |
0.0022603274 |
0.0006632656 |
3.4079 |
2.001437e-03 |
0.01523938 |
| 289 |
SUN1 |
0.0017101931 |
0.0005034365 |
3.3970 |
2.058187e-03 |
0.01523938 |
| 305 |
NUDT21 |
0.0016457420 |
0.0004861225 |
3.3854 |
2.120597e-03 |
0.01523938 |
| 17 |
ANAPC4 |
0.0006206811 |
0.0001834687 |
3.3830 |
2.133806e-03 |
0.01523938 |
| 314 |
TM2D2 |
0.0008956957 |
0.0002651008 |
3.3787 |
2.157768e-03 |
0.01523938 |
| 243 |
NUS1 |
0.0010718193 |
0.0003178390 |
3.3722 |
2.194113e-03 |
0.01523938 |
| 119 |
RPS25 |
0.0015106862 |
0.0004484341 |
3.3688 |
2.213417e-03 |
0.01523938 |
| 392 |
C1orf174 |
0.0020781184 |
0.0006171776 |
3.3671 |
2.222953e-03 |
0.01523938 |
| 387 |
FOXJ3 |
0.0013808418 |
0.0004102588 |
3.3658 |
2.230679e-03 |
0.01523938 |
| 94 |
RWDD1 |
0.0011509067 |
0.0003435451 |
3.3501 |
2.322472e-03 |
0.01523938 |
| 247 |
KLF10 |
0.0017230728 |
0.0005145131 |
3.3489 |
2.329339e-03 |
0.01523938 |
| 60 |
HNRNPH3 |
0.0012647372 |
0.0003776976 |
3.3485 |
2.331696e-03 |
0.01523938 |
| 30 |
ISOC1 |
0.0018346516 |
0.0005484091 |
3.3454 |
2.350554e-03 |
0.01523938 |
| 231 |
PTS |
0.0014024193 |
0.0004198042 |
3.3407 |
2.379418e-03 |
0.01523938 |
| 301 |
CUL5 |
0.0007362499 |
0.0002207817 |
3.3347 |
2.415750e-03 |
0.01523938 |
| 150 |
VIMP |
0.0008271301 |
0.0002495984 |
3.3138 |
2.548601e-03 |
0.01523938 |
| 313 |
ZBTB49 |
0.0011136255 |
0.0003364800 |
3.3096 |
2.576203e-03 |
0.01523938 |
| 151 |
PRKAA1 |
0.0009691372 |
0.0002938474 |
3.2981 |
2.653326e-03 |
0.01523938 |
| 353 |
X15.Sep |
0.0014147154 |
0.0004289789 |
3.2979 |
2.654883e-03 |
0.01523938 |
| 341 |
C8orf59 |
0.0006719449 |
0.0002038512 |
3.2963 |
2.665864e-03 |
0.01523938 |
| 88 |
GTF2H1 |
0.0008914960 |
0.0002704685 |
3.2961 |
2.666776e-03 |
0.01523938 |
| 90 |
NAA25 |
0.0005421613 |
0.0001646802 |
3.2922 |
2.693546e-03 |
0.01523938 |
| 217 |
MANF |
0.0012190842 |
0.0003703170 |
3.2920 |
2.694961e-03 |
0.01523938 |
| 24 |
MTMR1 |
0.0008711950 |
0.0002646723 |
3.2916 |
2.697734e-03 |
0.01523938 |
| 376 |
TRIM33 |
0.0008202596 |
0.0002493568 |
3.2895 |
2.712223e-03 |
0.01523938 |
| 250 |
CNOT8 |
0.0014254054 |
0.0004341254 |
3.2834 |
2.754824e-03 |
0.01523938 |
| 180 |
THUMPD2 |
0.0009646625 |
0.0002940902 |
3.2802 |
2.777669e-03 |
0.01523938 |
| 212 |
EAF1 |
0.0016338107 |
0.0004987928 |
3.2755 |
2.810651e-03 |
0.01523938 |
| 299 |
TRUB1 |
0.0013293937 |
0.0004059108 |
3.2751 |
2.813820e-03 |
0.01523938 |
| 31 |
ARFGEF1 |
0.0008873710 |
0.0002727469 |
3.2535 |
2.973176e-03 |
0.01523938 |
| 248 |
PTPRN2 |
0.0012859617 |
0.0003954155 |
3.2522 |
2.982887e-03 |
0.01523938 |
| 258 |
MFSD14A |
0.0009360301 |
0.0002878697 |
3.2516 |
2.987465e-03 |
0.01523938 |
| 152 |
SEC61G |
0.0020590384 |
0.0006333877 |
3.2508 |
2.993099e-03 |
0.01523938 |
| 262 |
SLC35B2 |
0.0021351364 |
0.0006575850 |
3.2469 |
3.022921e-03 |
0.01523938 |
| 340 |
MEX3C |
0.0011805756 |
0.0003636831 |
3.2462 |
3.028851e-03 |
0.01523938 |
| 375 |
MAFG |
0.0014387699 |
0.0004442684 |
3.2385 |
3.088315e-03 |
0.01523938 |
| 106 |
ACVR1 |
0.0013603959 |
0.0004207132 |
3.2335 |
3.127532e-03 |
0.01523938 |
| 227 |
MFSD14B |
0.0015164252 |
0.0004705336 |
3.2228 |
3.214189e-03 |
0.01523938 |
| 175 |
CCDC90B |
0.0010242649 |
0.0003179770 |
3.2212 |
3.227145e-03 |
0.01523938 |
| 8 |
IFNGR1 |
0.0014060444 |
0.0004367476 |
3.2194 |
3.242234e-03 |
0.01523938 |
| 145 |
PSMG2 |
0.0011941514 |
0.0003712043 |
3.2170 |
3.261912e-03 |
0.01523938 |
| 342 |
FAM91A1 |
0.0010357615 |
0.0003224243 |
3.2124 |
3.299726e-03 |
0.01523938 |
| 124 |
PROSER1 |
0.0011413673 |
0.0003557079 |
3.2087 |
3.330773e-03 |
0.01523938 |
| 325 |
ZNF680 |
0.0011950861 |
0.0003727203 |
3.2064 |
3.350501e-03 |
0.01523938 |
| 158 |
CYP2J2 |
0.0014743566 |
0.0004618841 |
3.1920 |
3.474306e-03 |
0.01553088 |
| 421 |
GTF2H5 |
0.0011014230 |
0.0003452210 |
3.1905 |
3.488059e-03 |
0.01553088 |
| 133 |
EBPL |
0.0007688893 |
0.0002420693 |
3.1763 |
3.615157e-03 |
0.01553088 |
| 195 |
RB1 |
0.0013292562 |
0.0004189996 |
3.1725 |
3.650600e-03 |
0.01553088 |
| 87 |
NDUFC1 |
0.0015680501 |
0.0004967129 |
3.1569 |
3.797027e-03 |
0.01553088 |
| 366 |
GTF2F2 |
0.0006693549 |
0.0002121712 |
3.1548 |
3.816842e-03 |
0.01553088 |
| 38 |
SCARF1 |
0.0014814375 |
0.0004696206 |
3.1545 |
3.819211e-03 |
0.01553088 |
| 383 |
TXNRD1 |
0.0007296310 |
0.0002314590 |
3.1523 |
3.840710e-03 |
0.01553088 |
| 50 |
SLC25A24 |
0.0010227851 |
0.0003250847 |
3.1462 |
3.900144e-03 |
0.01553088 |
| 297 |
PRDX3 |
0.0018207059 |
0.0005790791 |
3.1441 |
3.920511e-03 |
0.01553088 |
| 377 |
S100A10 |
0.0010558993 |
0.0003358958 |
3.1435 |
3.926508e-03 |
0.01553088 |
| 166 |
SCYL2 |
0.0004753143 |
0.0001513106 |
3.1413 |
3.948456e-03 |
0.01553088 |
| 373 |
PPTC7 |
0.0006609633 |
0.0002104917 |
3.1401 |
3.960633e-03 |
0.01553088 |
| 3 |
DYRK4 |
0.0008905403 |
0.0002836823 |
3.1392 |
3.969352e-03 |
0.01553088 |
| 202 |
SMAD4 |
0.0009160672 |
0.0002919420 |
3.1378 |
3.983123e-03 |
0.01553088 |
| 42 |
UBE2T |
0.0015601886 |
0.0004983782 |
3.1305 |
4.056945e-03 |
0.01553088 |
| 165 |
CAB39 |
0.0014119311 |
0.0004512431 |
3.1290 |
4.072774e-03 |
0.01553088 |
| 380 |
ZNF251 |
0.0009688300 |
0.0003106621 |
3.1186 |
4.180316e-03 |
0.01553088 |
| 105 |
SF3B6 |
0.0013678870 |
0.0004390451 |
3.1156 |
4.211910e-03 |
0.01553088 |
| 274 |
NCSTN |
0.0020092480 |
0.0006449629 |
3.1153 |
4.215107e-03 |
0.01553088 |
| 184 |
VWA9 |
0.0016196039 |
0.0005201712 |
3.1136 |
4.233056e-03 |
0.01553088 |
| 210 |
CALM2 |
0.0012007113 |
0.0003858570 |
3.1118 |
4.252140e-03 |
0.01553088 |
| 236 |
BAG3 |
0.0015235464 |
0.0004904106 |
3.1067 |
4.307136e-03 |
0.01553088 |
| 409 |
ARFGAP3 |
0.0006602537 |
0.0002126433 |
3.1050 |
4.325440e-03 |
0.01553088 |
| 399 |
NRAS |
0.0020393811 |
0.0006573334 |
3.1025 |
4.352340e-03 |
0.01553088 |
| 315 |
PDCD6IP |
0.0009606885 |
0.0003098034 |
3.1010 |
4.369207e-03 |
0.01553088 |
| 351 |
IGIP |
0.0014864750 |
0.0004813413 |
3.0882 |
4.511031e-03 |
0.01590138 |
| 188 |
KIF21A |
0.0008225421 |
0.0002668000 |
3.0830 |
4.570055e-03 |
0.01594970 |
| 173 |
CPEB2 |
0.0009758515 |
0.0003167975 |
3.0804 |
4.600150e-03 |
0.01594970 |
| 199 |
SLC39A6 |
0.0008420206 |
0.0002741051 |
3.0719 |
4.698511e-03 |
0.01614344 |
| 404 |
LINC00998 |
0.0012653174 |
0.0004122881 |
3.0690 |
4.732356e-03 |
0.01614344 |
| 413 |
KIAA1147 |
0.0005963581 |
0.0001948689 |
3.0603 |
4.836231e-03 |
0.01631843 |
| 241 |
RPIA |
0.0013338088 |
0.0004361319 |
3.0583 |
4.860810e-03 |
0.01631843 |
| 229 |
LIN7C |
0.0010573735 |
0.0003469251 |
3.0478 |
4.988630e-03 |
0.01661567 |
| 129 |
TNFRSF10B |
0.0012773843 |
0.0004209555 |
3.0345 |
5.157071e-03 |
0.01704251 |
| 45 |
TIGAR |
0.0010053362 |
0.0003328995 |
3.0199 |
5.346700e-03 |
0.01713558 |
| 28 |
OAT |
0.0019111001 |
0.0006332720 |
3.0178 |
5.374885e-03 |
0.01713558 |
| 203 |
CREG1 |
0.0010308321 |
0.0003421173 |
3.0131 |
5.438186e-03 |
0.01713558 |
| 144 |
MTX2 |
0.0014420886 |
0.0004787614 |
3.0121 |
5.451289e-03 |
0.01713558 |
| 391 |
CAPZA2 |
0.0006620910 |
0.0002198170 |
3.0120 |
5.452839e-03 |
0.01713558 |
| 47 |
PCNP |
0.0007909625 |
0.0002627273 |
3.0106 |
5.472129e-03 |
0.01713558 |
| 123 |
PLEKHG1 |
0.0012053269 |
0.0004006892 |
3.0081 |
5.505435e-03 |
0.01713558 |
| 61 |
ASCC2 |
0.0005699803 |
0.0001894976 |
3.0078 |
5.509310e-03 |
0.01713558 |
| 300 |
CCT2 |
0.0009046769 |
0.0003019182 |
2.9964 |
5.667217e-03 |
0.01740464 |
| 269 |
EFCAB14 |
0.0008540047 |
0.0002850813 |
2.9957 |
5.678111e-03 |
0.01740464 |
| 292 |
AQP3 |
0.0024864677 |
0.0008311654 |
2.9915 |
5.736091e-03 |
0.01742595 |
| 130 |
B4GALT4 |
0.0017972457 |
0.0006012187 |
2.9893 |
5.767453e-03 |
0.01742595 |
| 260 |
AASDH |
0.0010521169 |
0.0003530848 |
2.9798 |
5.905099e-03 |
0.01766583 |
| 349 |
SIAH2 |
0.0012350764 |
0.0004147259 |
2.9781 |
5.930372e-03 |
0.01766583 |
| 310 |
PDHB |
0.0006331924 |
0.0002133770 |
2.9675 |
6.087009e-03 |
0.01797551 |
| 98 |
PAPD7 |
0.0010828292 |
0.0003651628 |
2.9653 |
6.119321e-03 |
0.01797551 |
| 69 |
POFUT1 |
0.0008892187 |
0.0003004084 |
2.9600 |
6.199715e-03 |
0.01808606 |
| 365 |
COMMD6 |
0.0018464027 |
0.0006249340 |
2.9546 |
6.283824e-03 |
0.01820587 |
| 272 |
JAK1 |
0.0004771416 |
0.0001619528 |
2.9462 |
6.414628e-03 |
0.01845842 |
| 257 |
EEF1A1 |
0.0010993766 |
0.0003741478 |
2.9383 |
6.539155e-03 |
0.01868961 |
| 159 |
RNF138 |
0.0013564009 |
0.0004627028 |
2.9315 |
6.650410e-03 |
0.01888002 |
| 239 |
MED21 |
0.0010091901 |
0.0003450439 |
2.9248 |
6.759829e-03 |
0.01888272 |
| 306 |
GLOD4 |
0.0005854801 |
0.0002003545 |
2.9222 |
6.802964e-03 |
0.01888272 |
| 205 |
PFDN2 |
0.0005112322 |
0.0001749813 |
2.9216 |
6.812661e-03 |
0.01888272 |
| 2 |
RANBP9 |
0.0009830117 |
0.0003367879 |
2.9188 |
6.860434e-03 |
0.01888272 |
| 276 |
CGGBP1 |
0.0005220411 |
0.0001790398 |
2.9158 |
6.911080e-03 |
0.01888272 |
| 284 |
FBXO8 |
0.0010488456 |
0.0003597726 |
2.9153 |
6.919202e-03 |
0.01888272 |
| 191 |
TDG |
0.0006282354 |
0.0002162190 |
2.9056 |
7.086209e-03 |
0.01921453 |
| 281 |
RCHY1 |
0.0011626251 |
0.0004012663 |
2.8974 |
7.228896e-03 |
0.01947658 |
| 138 |
L3HYPDH |
0.0012341812 |
0.0004272335 |
2.8888 |
7.382509e-03 |
0.01967307 |
| 20 |
ATG5 |
0.0010437581 |
0.0003614008 |
2.8881 |
7.394842e-03 |
0.01967307 |
| 420 |
LIX1L |
0.0017478761 |
0.0006061773 |
2.8834 |
7.479139e-03 |
0.01971243 |
| 52 |
TMED2 |
0.0009425678 |
0.0003270372 |
2.8821 |
7.502842e-03 |
0.01971243 |
| 348 |
PRKRA |
0.0008246032 |
0.0002867553 |
2.8756 |
7.622728e-03 |
0.01990379 |
| 25 |
ASUN |
0.0005893108 |
0.0002053001 |
2.8705 |
7.718861e-03 |
0.02003115 |
| 84 |
EIF4H |
0.0007529396 |
0.0002629158 |
2.8638 |
7.845261e-03 |
0.02023503 |
| 37 |
TSG101 |
0.0008556847 |
0.0002999327 |
2.8529 |
8.055401e-03 |
0.02054157 |
| 142 |
LSM8 |
0.0004747220 |
0.0001665490 |
2.8503 |
8.105944e-03 |
0.02054157 |
| 324 |
OXSR1 |
0.0006607591 |
0.0002318332 |
2.8501 |
8.109791e-03 |
0.02054157 |
| 295 |
MICU2 |
0.0004281525 |
0.0001503710 |
2.8473 |
8.165881e-03 |
0.02056052 |
| 279 |
RPL22L1 |
0.0016009073 |
0.0005654542 |
2.8312 |
8.491058e-03 |
0.02117421 |
| 56 |
NECAP1 |
0.0012772309 |
0.0004512736 |
2.8303 |
8.509731e-03 |
0.02117421 |
| 1 |
LAMP2 |
0.0007791179 |
0.0002762508 |
2.8203 |
8.716982e-03 |
0.02144240 |
| 253 |
PXYLP1 |
0.0008543575 |
0.0003029382 |
2.8202 |
8.718895e-03 |
0.02144240 |
| 312 |
FAM84B |
0.0008070957 |
0.0002866056 |
2.8160 |
8.807526e-03 |
0.02153516 |
| 252 |
FZD7 |
0.0010797161 |
0.0003847655 |
2.8062 |
9.020077e-03 |
0.02187080 |
| 360 |
AP3M1 |
0.0008247862 |
0.0002943417 |
2.8021 |
9.108086e-03 |
0.02187080 |
| 7 |
DERA |
0.0015372657 |
0.0005487559 |
2.8014 |
9.125084e-03 |
0.02187080 |
| 107 |
LANCL1 |
0.0008229414 |
0.0002941692 |
2.7975 |
9.210199e-03 |
0.02187080 |
| 270 |
BSDC1 |
0.0009443511 |
0.0003376053 |
2.7972 |
9.216987e-03 |
0.02187080 |
| 378 |
AKAP17A |
0.0006211350 |
0.0002221915 |
2.7955 |
9.255020e-03 |
0.02187080 |
| 55 |
SLC23A2 |
0.0012708198 |
0.0004551888 |
2.7919 |
9.336520e-03 |
0.02188528 |
| 21 |
ALDH18A1 |
0.0015523029 |
0.0005566590 |
2.7886 |
9.409701e-03 |
0.02188528 |
| 363 |
ZBTB6 |
0.0007549784 |
0.0002707654 |
2.7883 |
9.416364e-03 |
0.02188528 |
| 121 |
MYL12B |
0.0013006496 |
0.0004678226 |
2.7802 |
9.601320e-03 |
0.02219322 |
| 230 |
CPSF7 |
0.0010242681 |
0.0003695566 |
2.7716 |
9.801747e-03 |
0.02244758 |
| 104 |
EPB41L5 |
0.0006186529 |
0.0002233299 |
2.7701 |
9.836697e-03 |
0.02244758 |
| 330 |
HEG1 |
0.0006345267 |
0.0002291788 |
2.7687 |
9.870567e-03 |
0.02244758 |
| 369 |
ZNF548 |
0.0007221371 |
0.0002618061 |
2.7583 |
1.011983e-02 |
0.02283202 |
| 283 |
ANXA5 |
0.0007469359 |
0.0002709090 |
2.7571 |
1.014756e-02 |
0.02283202 |
| 178 |
GTF2B |
0.0007137483 |
0.0002601489 |
2.7436 |
1.048136e-02 |
0.02345827 |
| 303 |
SEC11C |
0.0008469506 |
0.0003104019 |
2.7286 |
1.086474e-02 |
0.02418834 |
| 78 |
DECR1 |
0.0010005443 |
0.0003670581 |
2.7258 |
1.093526e-02 |
0.02421787 |
| 89 |
BIN2 |
0.0009252361 |
0.0003398357 |
2.7226 |
1.102022e-02 |
0.02427892 |
| 128 |
TMPO |
0.0007027689 |
0.0002597862 |
2.7052 |
1.148632e-02 |
0.02507713 |
| 115 |
TMEM59 |
0.0016856853 |
0.0006232566 |
2.7046 |
1.150110e-02 |
0.02507713 |
| 113 |
SRSF7 |
0.0008765040 |
0.0003246208 |
2.7001 |
1.162617e-02 |
0.02521985 |
| 282 |
RPN1 |
0.0010121517 |
0.0003756030 |
2.6947 |
1.177460e-02 |
0.02541152 |
| 374 |
ZSCAN25 |
0.0008008030 |
0.0002975731 |
2.6911 |
1.187622e-02 |
0.02550071 |
| 44 |
UBE2A |
0.0011436891 |
0.0004286749 |
2.6680 |
1.254483e-02 |
0.02680031 |
| 423 |
PIP4K2B |
0.0004148197 |
0.0001557941 |
2.6626 |
1.270423e-02 |
0.02690036 |
| 13 |
CLEC16A |
0.0005080311 |
0.0001908365 |
2.6621 |
1.271884e-02 |
0.02690036 |
| 344 |
UBE2N |
0.0008192498 |
0.0003085062 |
2.6555 |
1.291804e-02 |
0.02718572 |
| 15 |
THOC3 |
0.0013730551 |
0.0005187582 |
2.6468 |
1.318628e-02 |
0.02761285 |
| 135 |
RAP2C |
0.0006917094 |
0.0002625785 |
2.6343 |
1.358008e-02 |
0.02817289 |
| 354 |
HMCES |
0.0004771956 |
0.0001811621 |
2.6341 |
1.358693e-02 |
0.02817289 |
| 371 |
IARS |
0.0005890273 |
0.0002241224 |
2.6281 |
1.377745e-02 |
0.02842860 |
| 177 |
ADAM10 |
0.0007009500 |
0.0002669702 |
2.6256 |
1.386095e-02 |
0.02846204 |
| 249 |
SAMSN1 |
0.0008947513 |
0.0003411306 |
2.6229 |
1.394817e-02 |
0.02850278 |
| 214 |
LRIG1 |
0.0009280812 |
0.0003544493 |
2.6184 |
1.409686e-02 |
0.02866813 |
| 170 |
NDUFB5 |
0.0009413787 |
0.0003616017 |
2.6034 |
1.460098e-02 |
0.02955127 |
| 382 |
GFPT1 |
0.0004352290 |
0.0001681985 |
2.5876 |
1.514827e-02 |
0.03051294 |
| 54 |
DOCK9 |
0.0009181845 |
0.0003552886 |
2.5843 |
1.526369e-02 |
0.03059971 |
| 337 |
ZNF654 |
0.0004372436 |
0.0001699650 |
2.5726 |
1.568806e-02 |
0.03130211 |
| 171 |
HS6ST1 |
0.0011616253 |
0.0004526650 |
2.5662 |
1.592158e-02 |
0.03161892 |
| 245 |
MRPL39 |
0.0013391300 |
0.0005223661 |
2.5636 |
1.601823e-02 |
0.03166219 |
| 148 |
TAF4 |
0.0005904934 |
0.0002309129 |
2.5572 |
1.625682e-02 |
0.03198434 |
| 407 |
ALG13.AS1 |
0.0012404807 |
0.0004880769 |
2.5416 |
1.685658e-02 |
0.03238547 |
| 51 |
DDHD2 |
0.0006663264 |
0.0002622833 |
2.5405 |
1.689888e-02 |
0.03238547 |
| 120 |
PLAGL1 |
0.0005631792 |
0.0002217277 |
2.5400 |
1.691942e-02 |
0.03238547 |
| 79 |
INTS10 |
0.0006068336 |
0.0002389245 |
2.5399 |
1.692349e-02 |
0.03238547 |
| 93 |
C2CD5 |
0.0006058432 |
0.0002388042 |
2.5370 |
1.703600e-02 |
0.03238547 |
| 194 |
KANSL2 |
0.0008872758 |
0.0003497542 |
2.5369 |
1.704122e-02 |
0.03238547 |
| 201 |
MBD1 |
0.0005425321 |
0.0002138634 |
2.5368 |
1.704277e-02 |
0.03238547 |
| 140 |
SLC10A3 |
0.0009829393 |
0.0003875876 |
2.5360 |
1.707319e-02 |
0.03238547 |
| 189 |
PEX5 |
0.0012932405 |
0.0005123686 |
2.5240 |
1.755266e-02 |
0.03308346 |
| 58 |
CMTM6 |
0.0017058897 |
0.0006763425 |
2.5222 |
1.762628e-02 |
0.03308346 |
| 197 |
NCOA2 |
0.0008054192 |
0.0003197018 |
2.5193 |
1.774630e-02 |
0.03308346 |
| 261 |
DSCR3 |
0.0007514300 |
0.0002984882 |
2.5175 |
1.782122e-02 |
0.03308346 |
| 117 |
BCAS2 |
0.0006090178 |
0.0002420605 |
2.5160 |
1.788207e-02 |
0.03308346 |
| 316 |
ARL6IP1 |
0.0012345264 |
0.0004908098 |
2.5153 |
1.791043e-02 |
0.03308346 |
| 183 |
SPPL2A |
0.0003746729 |
0.0001491085 |
2.5128 |
1.801503e-02 |
0.03313199 |
| 339 |
PLEKHF2 |
0.0009489622 |
0.0003789851 |
2.5040 |
1.838314e-02 |
0.03366263 |
| 43 |
SLC25A43 |
0.0007730279 |
0.0003093247 |
2.4991 |
1.859005e-02 |
0.03389478 |
| 224 |
ZNF92 |
0.0008118875 |
0.0003252765 |
2.4960 |
1.872234e-02 |
0.03398949 |
| 103 |
INO80D |
0.0005541580 |
0.0002225594 |
2.4899 |
1.898425e-02 |
0.03431769 |
| 200 |
C18orf21 |
0.0005903150 |
0.0002378130 |
2.4823 |
1.932053e-02 |
0.03477695 |
| 379 |
IRAK4 |
0.0004210703 |
0.0001708270 |
2.4649 |
2.010277e-02 |
0.03594822 |
| 311 |
CMAHP |
0.0007431652 |
0.0003016023 |
2.4641 |
2.014120e-02 |
0.03594822 |
| 29 |
NDUFB4 |
0.0012061236 |
0.0004926986 |
2.4480 |
2.089158e-02 |
0.03713084 |
| 296 |
QSOX2 |
0.0007713730 |
0.0003164605 |
2.4375 |
2.139559e-02 |
0.03773607 |
| 238 |
ZFP36L2 |
0.0009926851 |
0.0004073066 |
2.4372 |
2.141054e-02 |
0.03773607 |
| 403 |
NAXD |
0.0006257749 |
0.0002581703 |
2.4239 |
2.206628e-02 |
0.03873044 |
| 206 |
POGZ |
0.0005290698 |
0.0002199662 |
2.4052 |
2.301626e-02 |
0.04023090 |
| 218 |
OCIAD2 |
0.0011568864 |
0.0004819161 |
2.4006 |
2.325806e-02 |
0.04048625 |
| 163 |
RNASEL |
0.0005132963 |
0.0002140144 |
2.3984 |
2.337249e-02 |
0.04051870 |
| 275 |
WDR26 |
0.0006515947 |
0.0002721005 |
2.3947 |
2.356992e-02 |
0.04069418 |
| 362 |
LRRC37B |
0.0005456514 |
0.0002290466 |
2.3823 |
2.423695e-02 |
0.04165622 |
| 222 |
RNF44 |
0.0008658175 |
0.0003638340 |
2.3797 |
2.437711e-02 |
0.04165622 |
| 190 |
POC1B |
0.0008908280 |
0.0003749501 |
2.3759 |
2.458843e-02 |
0.04165622 |
| 40 |
MYDGF |
0.0013760987 |
0.0005796144 |
2.3742 |
2.468211e-02 |
0.04165622 |
| 76 |
ZDHHC2 |
0.0008333087 |
0.0003511122 |
2.3733 |
2.472766e-02 |
0.04165622 |
| 402 |
CLIC1 |
0.0012607929 |
0.0005315114 |
2.3721 |
2.479704e-02 |
0.04165622 |
| 370 |
PNRC2 |
0.0003989600 |
0.0001682140 |
2.3717 |
2.481647e-02 |
0.04165622 |
| 237 |
UHMK1 |
0.0004286115 |
0.0001811670 |
2.3658 |
2.514684e-02 |
0.04204393 |
| 4 |
UFL1 |
0.0002919023 |
0.0001234915 |
2.3637 |
2.526484e-02 |
0.04207491 |
| 71 |
RBM3 |
0.0005036289 |
0.0002139201 |
2.3543 |
2.580482e-02 |
0.04278526 |
| 234 |
SLC25A4 |
0.0005374443 |
0.0002284328 |
2.3527 |
2.589368e-02 |
0.04278526 |
| 83 |
RHEB |
0.0007299891 |
0.0003113427 |
2.3446 |
2.636571e-02 |
0.04339570 |
| 304 |
NEMP1 |
0.0007306429 |
0.0003124816 |
2.3382 |
2.674752e-02 |
0.04359065 |
| 39 |
LMAN1 |
0.0004120478 |
0.0001762690 |
2.3376 |
2.678247e-02 |
0.04359065 |
| 221 |
BTF3 |
0.0007895802 |
0.0003380330 |
2.3358 |
2.689002e-02 |
0.04359065 |
| 192 |
NUP58 |
0.0003018967 |
0.0001292531 |
2.3357 |
2.689636e-02 |
0.04359065 |
| 95 |
E2F3 |
0.0004408303 |
0.0001903357 |
2.3161 |
2.809512e-02 |
0.04535968 |
| 331 |
STAT5B |
0.0005039565 |
0.0002201011 |
2.2897 |
2.978401e-02 |
0.04790355 |
| 167 |
TBC1D4 |
0.0005707604 |
0.0002512980 |
2.2712 |
3.101521e-02 |
0.04941936 |
| 322 |
PPP1CA |
0.0016181707 |
0.0007124900 |
2.2711 |
3.102207e-02 |
0.04941936 |
| 6 |
MDH1 |
0.0007345141 |
0.0003235255 |
2.2703 |
3.107695e-02 |
0.04941936 |
| 193 |
N4BP2L1 |
0.0006144075 |
0.0002727501 |
2.2526 |
3.230647e-02 |
0.05112888 |
| 160 |
TMED7 |
0.0007902107 |
0.0003510073 |
2.2513 |
3.240365e-02 |
0.05112888 |
| 298 |
GHITM |
0.0005344812 |
0.0002375786 |
2.2497 |
3.251458e-02 |
0.05112888 |
| 367 |
FAM92A1 |
0.0005762252 |
0.0002567619 |
2.2442 |
3.290777e-02 |
0.05155551 |
| 390 |
CIPC |
0.0008912699 |
0.0003982984 |
2.2377 |
3.337830e-02 |
0.05209971 |
| 168 |
ITM2B |
0.0004897186 |
0.0002203091 |
2.2229 |
3.447298e-02 |
0.05361055 |
| 416 |
NBPF11 |
0.0010286471 |
0.0004632914 |
2.2203 |
3.466590e-02 |
0.05371310 |
| 116 |
SWT1 |
0.0005573456 |
0.0002517846 |
2.2136 |
3.517542e-02 |
0.05430367 |
| 309 |
MAPK1IP1L |
0.0004050776 |
0.0001831922 |
2.2112 |
3.535626e-02 |
0.05437553 |
| 34 |
CDC42 |
0.0006636772 |
0.0003003585 |
2.2096 |
3.547907e-02 |
0.05437553 |
| 91 |
GOLT1B |
0.0006769670 |
0.0003078936 |
2.1987 |
3.632713e-02 |
0.05547429 |
| 172 |
FAM8A1 |
0.0007134686 |
0.0003249411 |
2.1957 |
3.656488e-02 |
0.05563650 |
| 246 |
ATP5J |
0.0006059132 |
0.0002764456 |
2.1918 |
3.687311e-02 |
0.05584547 |
| 100 |
CCNG1 |
0.0009476893 |
0.0004326103 |
2.1906 |
3.696627e-02 |
0.05584547 |
| 264 |
SLC37A3 |
0.0006772117 |
0.0003095265 |
2.1879 |
3.718503e-02 |
0.05597604 |
| 265 |
PPP1R15B |
0.0003703321 |
0.0001695817 |
2.1838 |
3.751496e-02 |
0.05627244 |
| 232 |
ACAD8 |
0.0008073511 |
0.0003708445 |
2.1771 |
3.806320e-02 |
0.05689305 |
| 319 |
C1GALT1C1 |
0.0003654775 |
0.0001687227 |
2.1661 |
3.896687e-02 |
0.05803868 |
| 122 |
ALG2 |
0.0005243923 |
0.0002426652 |
2.1610 |
3.940165e-02 |
0.05848034 |
| 267 |
BTG2 |
0.0008326295 |
0.0003874272 |
2.1491 |
4.041372e-02 |
0.05959607 |
| 67 |
PRELID3B |
0.0007507225 |
0.0003493557 |
2.1489 |
4.043516e-02 |
0.05959607 |
| 225 |
LACTB2 |
0.0006140509 |
0.0002877463 |
2.1340 |
4.173969e-02 |
0.06130517 |
| 64 |
CCNB1IP1 |
0.0005475081 |
0.0002568260 |
2.1318 |
4.193364e-02 |
0.06137692 |
| 220 |
SRD5A1 |
0.0005940853 |
0.0002803846 |
2.1188 |
4.310927e-02 |
0.06288007 |
| 176 |
BUD13 |
0.0003578329 |
0.0001692056 |
2.1148 |
4.348059e-02 |
0.06320375 |
| 361 |
NSMCE3 |
0.0007652536 |
0.0003630958 |
2.1076 |
4.414937e-02 |
0.06395611 |
| 26 |
TAF2 |
0.0003690563 |
0.0001753284 |
2.1049 |
4.439658e-02 |
0.06409472 |
| 263 |
TAB3 |
0.0003835229 |
0.0001828200 |
2.0978 |
4.507065e-02 |
0.06484655 |
| 110 |
KDM3A |
0.0004990147 |
0.0002381331 |
2.0955 |
4.528908e-02 |
0.06493993 |
| 102 |
ARL6 |
0.0004884750 |
0.0002333599 |
2.0932 |
4.550977e-02 |
0.06503593 |
| 345 |
ARL6IP6 |
0.0005010816 |
0.0002423068 |
2.0680 |
4.799464e-02 |
0.06835601 |
| 336 |
GPR171 |
-0.0006351095 |
0.0003075104 |
-2.0653 |
4.826082e-02 |
0.06850445 |
| 198 |
GLYR1 |
0.0003953837 |
0.0001919390 |
2.0599 |
4.880808e-02 |
0.06890109 |
| 48 |
CHMP2B |
0.0006023677 |
0.0002924997 |
2.0594 |
4.886602e-02 |
0.06890109 |
| 68 |
TM9SF4 |
0.0003141463 |
0.0001529613 |
2.0538 |
4.944360e-02 |
0.06948386 |
| 70 |
METTL4 |
0.0003353403 |
0.0001641694 |
2.0426 |
5.060449e-02 |
0.07087980 |
| 111 |
NOL10 |
0.0005385585 |
0.0002638952 |
2.0408 |
5.079938e-02 |
0.07091795 |
| 277 |
EIF4E3 |
0.0006749756 |
0.0003312498 |
2.0377 |
5.113291e-02 |
0.07114876 |
| 226 |
EBAG9 |
0.0002531786 |
0.0001249288 |
2.0266 |
5.232500e-02 |
0.07256877 |
| 291 |
KIAA0196 |
0.0006748153 |
0.0003343753 |
2.0181 |
5.324999e-02 |
0.07361029 |
| 242 |
CEBPG |
0.0003382728 |
0.0001691162 |
2.0002 |
5.525800e-02 |
0.07613724 |
| 66 |
GINS1 |
0.0004133047 |
0.0002070490 |
1.9962 |
5.572380e-02 |
0.07652977 |
| 256 |
RPL30 |
0.0010584229 |
0.0005370339 |
1.9709 |
5.869738e-02 |
0.08035272 |
| 9 |
TBPL1 |
0.0005922521 |
0.0003013754 |
1.9652 |
5.938660e-02 |
0.08103398 |
| 92 |
CLEC4A |
0.0006298252 |
0.0003218304 |
1.9570 |
6.038429e-02 |
0.08213040 |
| 73 |
UBFD1 |
0.0004220478 |
0.0002163656 |
1.9506 |
6.117573e-02 |
0.08294017 |
| 368 |
CERKL |
0.0006413762 |
0.0003316120 |
1.9341 |
6.326380e-02 |
0.08549708 |
| 318 |
XKR6 |
0.0007320168 |
0.0003794257 |
1.9293 |
6.388776e-02 |
0.08606536 |
| 398 |
TRIM59 |
0.0004475526 |
0.0002331387 |
1.9197 |
6.513994e-02 |
0.08747363 |
| 112 |
RAB3GAP1 |
0.0001484510 |
0.0000775788 |
1.9136 |
6.595167e-02 |
0.08828341 |
| 343 |
ZDHHC13 |
0.0004121858 |
0.0002163343 |
1.9053 |
6.705519e-02 |
0.08947744 |
| 99 |
ARSB |
0.0007622662 |
0.0004006705 |
1.9025 |
6.743992e-02 |
0.08970782 |
| 207 |
INTS7 |
0.0004438954 |
0.0002389414 |
1.8578 |
7.374883e-02 |
0.09779233 |
| 401 |
PPP1CB |
0.0005954306 |
0.0003243724 |
1.8356 |
7.705333e-02 |
0.10185487 |
| 357 |
SH2D1A |
-0.0010664737 |
0.0005841488 |
-1.8257 |
7.858091e-02 |
0.10355055 |
| 46 |
EPB41L2 |
0.0004749644 |
0.0002605469 |
1.8230 |
7.900557e-02 |
0.10378682 |
| 219 |
NAF1 |
0.0003232984 |
0.0001781255 |
1.8150 |
8.025013e-02 |
0.10509537 |
| 328 |
LRRN3 |
0.0005224470 |
0.0002891260 |
1.8070 |
8.152216e-02 |
0.10643170 |
| 411 |
IFNG.AS1 |
-0.0005213398 |
0.0002889400 |
-1.8043 |
8.194942e-02 |
0.10666032 |
| 65 |
PCIF1 |
0.0003926356 |
0.0002184605 |
1.7973 |
8.308496e-02 |
0.10780656 |
| 364 |
RPS23 |
0.0009191039 |
0.0005167797 |
1.7785 |
8.617954e-02 |
0.11147995 |
| 126 |
ELF1 |
0.0002563900 |
0.0001448954 |
1.7695 |
8.770487e-02 |
0.11310720 |
| 271 |
SLC37A1 |
0.0005017942 |
0.0002841260 |
1.7661 |
8.828227e-02 |
0.11350578 |
| 414 |
CTD.2501E16.2 |
-0.0004297026 |
0.0002450789 |
-1.7533 |
9.048961e-02 |
0.11583623 |
| 400 |
LEPROT |
0.0003988975 |
0.0002276230 |
1.7524 |
9.064254e-02 |
0.11583623 |
| 223 |
PRIM2 |
0.0003960630 |
0.0002319783 |
1.7073 |
9.882851e-02 |
0.12591705 |
| 77 |
NBN |
0.0002593332 |
0.0001538730 |
1.6854 |
1.030318e-01 |
0.13087824 |
| 86 |
MAP3K8 |
0.0003230892 |
0.0001926483 |
1.6771 |
1.046552e-01 |
0.13254236 |
| 23 |
GLTSCR1 |
0.0005455170 |
0.0003304745 |
1.6507 |
1.099723e-01 |
0.13886056 |
| 146 |
INO80 |
0.0003574968 |
0.0002176332 |
1.6427 |
1.116388e-01 |
0.14054529 |
| 352 |
HMGN4 |
0.0003790929 |
0.0002328074 |
1.6284 |
1.146514e-01 |
0.14390966 |
| 63 |
RPS6KA5 |
0.0003569852 |
0.0002208474 |
1.6164 |
1.172134e-01 |
0.14669020 |
| 355 |
TMEM50A |
0.0003298804 |
0.0002059599 |
1.6017 |
1.204513e-01 |
0.15029767 |
| 216 |
ATG3 |
0.0002814391 |
0.0001763578 |
1.5958 |
1.217507e-01 |
0.15147222 |
| 321 |
JMJD1C |
0.0002355853 |
0.0001488240 |
1.5830 |
1.246574e-01 |
0.15463372 |
| 287 |
ACSL6 |
0.0003418470 |
0.0002214593 |
1.5436 |
1.339107e-01 |
0.16562633 |
| 75 |
SGK3 |
0.0002287546 |
0.0001486286 |
1.5391 |
1.350053e-01 |
0.16649339 |
| 334 |
TLR1 |
0.0003310792 |
0.0002182402 |
1.5170 |
1.404668e-01 |
0.17272522 |
| 22 |
ELMO2 |
-0.0002208026 |
0.0001496608 |
-1.4754 |
1.512749e-01 |
0.18547618 |
| 422 |
RP11.5C23.1 |
0.0004822673 |
0.0003328020 |
1.4491 |
1.584145e-01 |
0.19366864 |
| 127 |
SERP1 |
0.0002765769 |
0.0001912003 |
1.4465 |
1.591312e-01 |
0.19398417 |
| 294 |
REEP3 |
0.0002490233 |
0.0001772586 |
1.4049 |
1.710609e-01 |
0.20792743 |
| 97 |
COX7A2 |
0.0003770975 |
0.0002690354 |
1.4017 |
1.720036e-01 |
0.20847423 |
| 266 |
ELK4 |
0.0002358329 |
0.0001685073 |
1.3995 |
1.726328e-01 |
0.20850472 |
| 16 |
MSMO1 |
0.0006178092 |
0.0004418429 |
1.3983 |
1.730146e-01 |
0.20850472 |
| 273 |
SLC30A7 |
0.0002524850 |
0.0001813272 |
1.3924 |
1.747533e-01 |
0.20911244 |
| 240 |
TXNDC11 |
0.0004285994 |
0.0003079821 |
1.3916 |
1.749901e-01 |
0.20911244 |
| 179 |
RABGGTB |
0.0002572125 |
0.0001848325 |
1.3916 |
1.750019e-01 |
0.20911244 |
| 386 |
PNP |
0.0005169485 |
0.0003741499 |
1.3817 |
1.780016e-01 |
0.21209772 |
| 139 |
FAM78A |
-0.0004110140 |
0.0003055129 |
-1.3453 |
1.893154e-01 |
0.22494495 |
| 233 |
KIN |
-0.0001571441 |
0.0001174608 |
-1.3378 |
1.917129e-01 |
0.22715564 |
| 406 |
LINC00623 |
0.0004825797 |
0.0003664253 |
1.3170 |
1.985182e-01 |
0.23456201 |
| 157 |
TSPAN2 |
0.0003308056 |
0.0002531384 |
1.3068 |
2.019067e-01 |
0.23790121 |
| 259 |
SEC13 |
0.0003203131 |
0.0002464649 |
1.2996 |
2.043265e-01 |
0.24008365 |
| 57 |
PUS7 |
0.0003487348 |
0.0002698505 |
1.2923 |
2.068084e-01 |
0.24232670 |
| 302 |
TMX3 |
0.0001285896 |
0.0001035059 |
1.2423 |
2.244158e-01 |
0.26223167 |
| 388 |
SFMBT2 |
-0.0003342819 |
0.0002749787 |
-1.2157 |
2.342634e-01 |
0.27298460 |
| 41 |
ARHGAP15 |
0.0003028796 |
0.0002499343 |
1.2118 |
2.357025e-01 |
0.27390703 |
| 397 |
HLA.A |
-0.0003110477 |
0.0002589004 |
-1.2014 |
2.396529e-01 |
0.27772186 |
| 393 |
NAGA |
-0.0001797986 |
0.0001498661 |
-1.1997 |
2.402983e-01 |
0.27772186 |
| 155 |
ARNTL |
0.0002977453 |
0.0002553670 |
1.1660 |
2.534703e-01 |
0.29214698 |
| 153 |
KIAA0907 |
0.0002815062 |
0.0002448897 |
1.1495 |
2.600651e-01 |
0.29893349 |
| 418 |
RP11.154H23.3 |
0.0002438949 |
0.0002153350 |
1.1326 |
2.669758e-01 |
0.30604541 |
| 215 |
NFKBIZ |
0.0003477685 |
0.0003187559 |
1.0910 |
2.845648e-01 |
0.32532683 |
| 255 |
DCK |
0.0002361779 |
0.0002223772 |
1.0621 |
2.972833e-01 |
0.33895109 |
| 213 |
CSRNP1 |
0.0003158340 |
0.0002993308 |
1.0551 |
3.003840e-01 |
0.34156570 |
| 53 |
PGS1 |
0.0002443465 |
0.0002334440 |
1.0467 |
3.041886e-01 |
0.34496460 |
| 356 |
TBK1 |
0.0001635782 |
0.0001585079 |
1.0320 |
3.109100e-01 |
0.35164424 |
| 174 |
FCHSD2 |
0.0001757848 |
0.0001720343 |
1.0218 |
3.156229e-01 |
0.35602268 |
| 154 |
USPL1 |
0.0001802700 |
0.0001772060 |
1.0173 |
3.177253e-01 |
0.35744095 |
| 134 |
AMD1 |
0.0002048975 |
0.0002032442 |
1.0081 |
3.220230e-01 |
0.36131489 |
| 81 |
BET1 |
0.0001432647 |
0.0001431950 |
1.0005 |
3.256432e-01 |
0.36441022 |
| 162 |
CCDC146 |
-0.0002046587 |
0.0002063436 |
-0.9918 |
3.297727e-01 |
0.36805768 |
| 181 |
CENPO |
0.0002556448 |
0.0002606132 |
0.9809 |
3.350248e-01 |
0.37293548 |
| 118 |
LGALS8 |
-0.0001535076 |
0.0001596473 |
-0.9615 |
3.445104e-01 |
0.38248795 |
| 114 |
TIA1 |
0.0001340060 |
0.0001430689 |
0.9367 |
3.569461e-01 |
0.39525704 |
| 417 |
NBPF12 |
0.0002500393 |
0.0002936150 |
0.8516 |
4.016672e-01 |
0.44361682 |
| 228 |
NOTCH1 |
0.0002255744 |
0.0002745347 |
0.8217 |
4.182118e-01 |
0.46068643 |
| 405 |
AC093818.1 |
-0.0001544513 |
0.0001928562 |
-0.8009 |
4.299549e-01 |
0.47239201 |
| 254 |
FAM161B |
0.0001707463 |
0.0002155638 |
0.7921 |
4.349671e-01 |
0.47666079 |
| 72 |
FNDC3A |
-0.0000864837 |
0.0001127031 |
-0.7674 |
4.492914e-01 |
0.49108600 |
| 33 |
CLEC2D |
-0.0002886735 |
0.0003785102 |
-0.7627 |
4.520454e-01 |
0.49282270 |
| 317 |
EMB |
0.0002175476 |
0.0003087050 |
0.7047 |
4.868113e-01 |
0.52936032 |
| 32 |
FTSJ1 |
0.0001453912 |
0.0002112883 |
0.6881 |
4.970405e-01 |
0.53909780 |
| 235 |
PARP8 |
-0.0001145582 |
0.0001808481 |
-0.6334 |
5.315806e-01 |
0.57508592 |
| 59 |
FKBP5 |
0.0001195887 |
0.0001947815 |
0.6140 |
5.441959e-01 |
0.58723185 |
| 346 |
GRAMD1C |
0.0001536877 |
0.0002524835 |
0.6087 |
5.476277e-01 |
0.58943139 |
| 394 |
SYT15 |
-0.0001414527 |
0.0002354582 |
-0.6008 |
5.528355e-01 |
0.59352642 |
| 372 |
CTBP1.AS2 |
0.0000932044 |
0.0001606312 |
0.5802 |
5.663947e-01 |
0.60654418 |
| 396 |
LIN52 |
0.0001061371 |
0.0001892216 |
0.5609 |
5.793176e-01 |
0.61881658 |
| 208 |
EFNA3 |
0.0001452409 |
0.0002619324 |
0.5545 |
5.836408e-01 |
0.62186416 |
| 136 |
BTN2A2 |
0.0002092487 |
0.0003796075 |
0.5512 |
5.858526e-01 |
0.62265234 |
| 280 |
CD200R1 |
0.0001451742 |
0.0002794209 |
0.5196 |
6.074578e-01 |
0.64399663 |
| 27 |
SNX24 |
-0.0000721165 |
0.0001572330 |
-0.4587 |
6.500188e-01 |
0.68739486 |
| 308 |
MLST8 |
0.0001090875 |
0.0002483357 |
0.4393 |
6.638345e-01 |
0.70025432 |
| 286 |
ERAP1 |
0.0000753807 |
0.0001799174 |
0.4190 |
6.784319e-01 |
0.71387232 |
| 408 |
RP11.666F17.1 |
0.0001137887 |
0.0003055701 |
0.3724 |
7.124125e-01 |
0.74776793 |
| 335 |
GCSAM |
0.0000684795 |
0.0002141775 |
0.3197 |
7.515448e-01 |
0.78688976 |
| 82 |
TWISTNB |
-0.0000537111 |
0.0001749610 |
-0.3070 |
7.611231e-01 |
0.79495082 |
| 278 |
EIF5A2 |
0.0000648502 |
0.0002168951 |
0.2990 |
7.671531e-01 |
0.79927525 |
| 326 |
HPSE |
-0.0000651726 |
0.0002295999 |
-0.2839 |
7.786116e-01 |
0.80922045 |
| 320 |
SPSB1 |
-0.0000472106 |
0.0001794178 |
-0.2631 |
7.943754e-01 |
0.82358037 |
| 329 |
PARP15 |
-0.0000860351 |
0.0003765571 |
-0.2285 |
8.209350e-01 |
0.84903542 |
| 132 |
SPATA1 |
0.0000504419 |
0.0002296293 |
0.2197 |
8.277243e-01 |
0.85396927 |
| 290 |
TP53INP1 |
0.0000602933 |
0.0002936949 |
0.2053 |
8.388290e-01 |
0.86332041 |
| 80 |
OAZ1 |
0.0000337373 |
0.0001668469 |
0.2022 |
8.412182e-01 |
0.86367793 |
| 147 |
TEP1 |
0.0000376748 |
0.0002100193 |
0.1794 |
8.589254e-01 |
0.87972260 |
| 35 |
RDH11 |
-0.0000376852 |
0.0002357859 |
-0.1598 |
8.741639e-01 |
0.89316747 |
| 11 |
UBA6 |
0.0000182077 |
0.0001364712 |
0.1334 |
8.948172e-01 |
0.91206666 |
| 419 |
NBPF19 |
0.0000271767 |
0.0002230679 |
0.1218 |
9.039027e-01 |
0.91911256 |
| 161 |
BICDL1 |
0.0000301402 |
0.0002643958 |
0.1140 |
9.100541e-01 |
0.92314837 |
| 143 |
IRF5 |
0.0000333176 |
0.0003344932 |
0.0996 |
9.213667e-01 |
0.93238782 |
| 288 |
CREBRF |
-0.0000155241 |
0.0001662916 |
-0.0934 |
9.262863e-01 |
0.93512917 |
| 358 |
VPS33B |
-0.0000086162 |
0.0001557421 |
-0.0553 |
9.562737e-01 |
0.96149559 |
| 186 |
CNOT6L |
-0.0000072987 |
0.0001340006 |
-0.0545 |
9.569495e-01 |
0.96149559 |
| 384 |
BAZ1A |
0.0000101561 |
0.0001973896 |
0.0515 |
9.593305e-01 |
0.96160384 |
| 5 |
ZC3H3 |
0.0000042798 |
0.0002471585 |
0.0173 |
9.863072e-01 |
0.98630720 |
Compare the Associations between Genelists
gene_FunRegRaw <- function(gene_matrix, clinical_variable, genelistname,clin_var_name){
## number of gene to test, also the number of multiple test
n_gene = ncol(gene_matrix)
## outcome lm
outcome_lm = lapply(1:n_gene, function(i){
lm = lm(gene_matrix[,i]~ clinical_variable + isgs.rld.lin$age + isgs.rld.lin$sex )
coef = summary(lm)$coefficients[2, ]
return(coef)
})
outcome_lm = data.frame(matrix(unlist(outcome_lm), ncol = 4, byrow = TRUE,
dimnames = list(
c(colnames(gene_matrix)),
c("Estimate", "Std.Error", "t.statistic", "p.value"))))
# adjusted p-value
outcome_lm = outcome_lm %>%
dplyr::mutate(FDR = p.adjust(p.value, "BH", n_gene ),
names = colnames(gene_matrix)) %>%
dplyr::mutate(Estimate = round(Estimate, 10),
Std.Error = round(Std.Error, 10),
t.statistic = round(t.statistic,4)
)%>%
select(names, everything())
# sort by p.value
outcome_lm = outcome_lm[order(outcome_lm$p.value), ]
## sample size
size = length(clinical_variable) - sum(clinical_variable)
# ## summary table
# kable(outcome_lm,
# caption = paste("Top Genes from ", genelistname, " Associated with Outcome: ", clin_var_name,
# " by p.value", " (Sample Size = ", size, ") ", sep = "" , collapse = ""),
# digits = c(2,10,10,4,20,20))
return(outcome_lm)
}
### cd4 counts
################# CD4 Counts #################
## whole isgs
isgs.cd4 <- gene_FunRegRaw(as.matrix(isgs.rld.lin[,2:231]), isgs.rld.lin[,234], "Core ISGs", "CD4 Counts")
## betas
genesbeta.cd4 <- gene_FunRegRaw(as.matrix(genesbeta.rld.lin[,2:424]), genesbeta.rld.lin[,427], "IFN-beta Genes", "CD4 Counts")
## enchanced volcano plots
## volcano plot
rownames(isgs.cd4) <- isgs.cd4$names
EnhancedVolcano(isgs.cd4,
lab = rownames(isgs.cd4),
x = "Estimate",
y = "FDR",
FCcutoff = 0.002,
xlab = bquote("Effect Size"),
ylab = bquote(~-Log[10]~adjusted~italic(P)),
title = "Core ISGs: Association with CD4 Counts",
xlim = c(-0.003, 0.003),
ylim = c(0, -log10(10e-10)),
# adjust the legend
legend=c("NS","log2 Fold Change >= 0.002","adjusted p-value <= 0.05",
"adjusted p-value <= 0.05 & log2 Fold Change >= 0.002"),
pLabellingCutoff = 5e-2,
pCutoff = 5e-2,
## select labels to show
# selectLab = c("cg18587484","cg00803922", " cg19425295"),
## point and label size
transcriptPointSize = 2.0,
transcriptLabSize = 3.5,
#Modify border and remove gridlines
gridlines.major = FALSE,
gridlines.minor = FALSE,
border = "full",
borderWidth = 1.0,
borderColour = "black",
# the transparence of the dots
colAlpha = 0.8,
legendPosition = "bottom",
legendLabSize = 9,
legendIconSize = 3,
# connectors
DrawConnectors = TRUE,
#
widthConnectors = 0.3,
#
colConnectors = "grey40",
col = c("grey30", "forestgreen", "royalblue", "tomato")
)

## volcano plot
rownames(genesbeta.cd4) <- genesbeta.cd4$names
EnhancedVolcano(genesbeta.cd4,
lab = rownames(genesbeta.cd4),
x = "Estimate",
y = "FDR",
FCcutoff = 0.002,
xlab = bquote("Effect Size"),
ylab = bquote(~-Log[10]~adjusted~italic(P)),
title = "IFN-beta Genes: Association with CD4 Counts",
xlim = c(-0.003, 0.003),
ylim = c(0, -log10(10e-10)),
# adjust the legend
legend=c("NS","log2 Fold Change >= 0.002","adjusted p-value <= 0.05",
"adjusted p-value <= 0.05 & log2 Fold Change >= 0.002"),
pLabellingCutoff = 5e-2,
pCutoff = 5e-2,
## select labels to show
# selectLab = c("cg18587484","cg00803922", " cg19425295"),
## point and label size
transcriptPointSize = 2.0,
transcriptLabSize = 3.5,
#Modify border and remove gridlines
gridlines.major = FALSE,
gridlines.minor = FALSE,
border = "full",
borderWidth = 1.0,
borderColour = "black",
# the transparence of the dots
colAlpha = 0.8,
legendPosition = "bottom",
legendLabSize = 9,
legendIconSize = 3,
# connectors
DrawConnectors = TRUE,
#
widthConnectors = 0.3,
#
colConnectors = "grey40",
col = c("grey30", "forestgreen", "royalblue", "tomato")
)

### plot some genes
## plot counts of minimum padj
plotCounts(dds, gene=which.min(res$padj), intgroup="condition",
main = "EOMES")

## the list of edgeR DE genes
res.edger.order <- res.edger[order(res.edger$PValue), ]
res.edger.order <- res.edger.order %>% dplyr::mutate(Direction = ifelse(logFC > 0, "Up-regulated", "Down-regulated"))
rownames(res.edger.order) <- rownames(res.edger[order(res.edger$PValue), ])
kable(head(res.edger.order[,-2],10), digits = c(2,50,2,50,2))
| ENSG00000163508.12 |
3.49 |
2.089250e-31 |
EOMES |
4.155519e-27 |
Up-regulated |
| ENSG00000100450.12 |
3.88 |
4.613960e-27 |
GZMH |
4.588584e-23 |
Up-regulated |
| ENSG00000139187.9 |
2.46 |
9.193777e-23 |
KLRG1 |
6.095474e-19 |
Up-regulated |
| ENSG00000197057.8 |
3.15 |
1.906517e-19 |
DTHD1 |
7.870522e-16 |
Up-regulated |
| ENSG00000111801.15 |
1.57 |
1.978512e-19 |
BTN3A3 |
7.870522e-16 |
Up-regulated |
| ENSG00000153563.15 |
2.19 |
4.626093e-19 |
CD8A |
1.533550e-15 |
Up-regulated |
| ENSG00000105374.9 |
2.99 |
2.198960e-18 |
NKG7 |
6.248188e-15 |
Up-regulated |
| ENSG00000140853.15 |
1.81 |
2.566530e-18 |
NLRC5 |
6.381036e-15 |
Up-regulated |
| ENSG00000271503.5 |
2.17 |
2.777522e-17 |
CCL5 |
6.138324e-14 |
Up-regulated |
| ENSG00000168394.10 |
1.54 |
1.191253e-16 |
TAP1 |
2.369403e-13 |
Up-regulated |
## number of genes
nrow(res.edger.order[res.edger.order$FDR <= 0.05, ])
## [1] 4246
nrow(res.edger.order[(res.edger.order$FDR <= 0.05) & ((res.edger.order$logFC >= 1) | (res.edger.order$logFC <= -1 )), ])
## [1] 837
###
## summary results
summary(decideTests(et, p.value = 0.05,
lfc = 0))
## 2-1
## Down 1706
## NotSig 15644
## Up 2540
paste(1706+ 2540, "genes with FDR 0.05")
## [1] "4246 genes with FDR 0.05"
summary(decideTests(et, p.value = 0.05,
lfc = 1))
## 2-1
## Down 157
## NotSig 19053
## Up 680
paste(157 + 680, "genes with FDR 0.05")
## [1] "837 genes with FDR 0.05"
summary(decideTests(et, p.value = 0.05,
lfc = 2))
## 2-1
## Down 7
## NotSig 19786
## Up 97
## the results matrix with 0, 1, -1
# decideTests(et, p.value = 0.05, lfc = 1)
res.edger.05 <- res.edger.order[res.edger.order$FDR <= 0.05, ]
res.edger.05$Gene_ID <- rownames(res.edger.05)
dim(res.edger.05)
## [1] 4246 7
## the two cutoffs
res.edger.05.1 <- res.edger.order[(res.edger.order$FDR <= 0.05) & ((res.edger.order$logFC >= 1) | (res.edger.order$logFC <= -1 )), ]
res.edger.05.1$Gene_ID <- rownames(res.edger.05.1)
dim(res.edger.05.1)
## [1] 837 7
## merge the DE list with predefined genelist
############################ core ISGs#############################
isgs.edger.05 <- base::merge(res.edger.05, isgs, by = "Gene_ID")
dim(isgs.edger.05)
## [1] 117 8
write.csv(isgs.edger.05,
"~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/corr/isgs.edger.05.csv")
isgs.edger.05.1 <- base::merge(res.edger.05.1, isgs, by = "Gene_ID")
dim(isgs.edger.05.1)
## [1] 52 8
colnames(isgs.edger.05 )
## [1] "Gene_ID" "logFC" "logCPM" "PValue" "Symbol.x" "FDR"
## [7] "Direction" "Symbol.y"
## volcano plot
rownames(isgs.edger.05 ) <- isgs.edger.05$Symbol.x
EnhancedVolcano(isgs.edger.05 ,
lab = rownames(isgs.edger.05 ),
x = "logFC",
y = "FDR",
pCutoff = 5e-2,
FCcutoff = 1,
pLabellingCutoff = 5e-2,
## select labels to show
# selectLab = c("cg18587484","cg00803922", " cg19425295"),
## point and label size
transcriptPointSize = 2.0,
transcriptLabSize = 3.5,
xlab = bquote(~Log[2]~ "Fold Change"),
ylab = bquote(~-Log[10]~adjusted~italic(P)),
title = "Core ISGs: HIV Infected vs Health Control by edgeR",
#Modify border and remove gridlines
gridlines.major = FALSE,
gridlines.minor = FALSE,
border = "full",
borderWidth = 1.0,
borderColour = "black",
# the transparence of the dots
colAlpha = 0.8,
xlim = c(-4, 4),
ylim = c(0, -log10(10e-25)),
# adjust the legend
legend=c("NS","log2 Fold Change >= 1","adjusted p-value <= 0.05",
"adjusted p-value <= 0.05 & log2 Fold Change >= 1"),
legendPosition = "bottom",
legendLabSize = 9,
legendIconSize = 3,
# connectors
DrawConnectors = TRUE,
#
widthConnectors = 0.3,
#
colConnectors = "grey40",
col = c("grey30", "forestgreen", "royalblue", "tomato")
)

############################ ifn beta genes #############################
## DE genes in the core genesbeta list
## directions of regulation
genesbeta.edger.05 <- base::merge(res.edger.05, genesbeta, by = "Gene_ID")
dim(genesbeta.edger.05)
## [1] 130 8
write.csv(genesbeta.edger.05,
"~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/corr/genesbeta.edger.05.csv")
genesbeta.edger.05.1 <- base::merge(res.edger.05.1, genesbeta, by = "Gene_ID")
dim(genesbeta.edger.05.1)
## [1] 8 8
########## association ###########
###### still use rlog transformation of deseq2 normalized counts data ###############
## gene level dataset
#######
rlog.isgs.05 <- base::merge(var.rld, isgs.edger.05, by = "Gene_ID") %>% dplyr::mutate(Symbol = Symbol.x) %>%
select(-c(Symbol.x, Symbol.y))
dim(rlog.isgs.05)
## [1] 117 39
rlog.isgs.05.1 <- base::merge(var.rld, isgs.edger.05.1, by = "Gene_ID") %>%
dplyr::mutate(Symbol = Symbol.x) %>%
select(-c(Symbol.x, Symbol.y))
dim(rlog.isgs.05.1)
## [1] 52 39
#########
rlog.genesbeta.05 <- base::merge(var.rld, genesbeta.edger.05, by = "Gene_ID") %>%
dplyr::mutate(Symbol = Symbol.x) %>%
select(-c(Symbol.x, Symbol.y))
dim(rlog.genesbeta.05)
## [1] 130 39
rlog.genesbeta.05.1 <- base::merge(var.rld, genesbeta.edger.05.1, by = "Gene_ID") %>%
dplyr::mutate(Symbol = Symbol.x) %>%
select(-c(Symbol.x, Symbol.y))
dim(rlog.genesbeta.05.1)
## [1] 8 39
########### check the effect of regularized log ###############
## compare the effect of rlog
n <- which(rownames(cnts.deseq2) %in% rlog.isgs.05[1, 1])
n
## [1] 21
plot(density(as.numeric( cnts.deseq2[n,] )), main="normalized counts (DESeq2)", cex.main=2)

plot(density(as.numeric(rlog.isgs.05[1,2:33])), main="rlog", cex.main=2)

plot(density(rnorm(10000, 0, 1)), main="ideal", cex.main=2)

## mean and sd relationship
library(vsn)
meanSdPlot(as.matrix(cnts.deseq2), main="normalized counts (DESeq2)")

meanSdPlot(as.matrix(var.cnts.rld), main="rlog")

plot(1:2000, rep(5,2000), type = "l", main = "ideal")

## check number of participants in the association data
nrow(isgs.rld.lin[,2:231])
## [1] 32
## make data ready for linear regression
rlog.isgs.05.raw <- as.matrix(t(rlog.isgs.05[,2:33]))
colnames(rlog.isgs.05.raw) <- rlog.isgs.05$Symbol
## row id to column pid
rlog.isgs.05.raw <- data.frame(rlog.isgs.05.raw)
##
rlog.isgs.05.1.raw <- as.matrix(t(rlog.isgs.05.1[,2:33]))
colnames(rlog.isgs.05.1.raw) <- rlog.isgs.05.1$Symbol
## row id to column pid
rlog.isgs.05.1.raw <- data.frame(rlog.isgs.05.1.raw)
######### for genes beta
## make data ready for linear regression
rlog.genesbeta.05.raw <- as.matrix(t(rlog.genesbeta.05[,2:33]))
colnames(rlog.genesbeta.05.raw) <- rlog.genesbeta.05$Symbol
## row id to column pid
rlog.genesbeta.05.raw <- data.frame(rlog.genesbeta.05.raw)
##
rlog.genesbeta.05.1.raw <- as.matrix(t(rlog.genesbeta.05.1[,2:33]))
colnames(rlog.genesbeta.05.1.raw) <- rlog.genesbeta.05.1$Symbol
## row id to column pid
rlog.genesbeta.05.1.raw <- data.frame(rlog.genesbeta.05.1.raw)
## run test association
############ viral load ################
## whole isgs
gene_FunReg(as.matrix(rlog.isgs.05.raw), isgs.rld.lin[,235], "Core ISGs", "Plasma Viral Load")
Top Genes from Core ISGs Associated with Outcome: Plasma Viral Load by p.value (Sample Size = NA)
| 107 |
ASAH2B |
7.9078e-06 |
2.2198e-06 |
3.5624 |
0.002836082 |
0.3318216 |
| 101 |
TDRD7 |
6.9213e-06 |
3.0309e-06 |
2.2836 |
0.037390883 |
0.9784102 |
| 25 |
TRIM38 |
-1.9743e-06 |
8.6700e-07 |
-2.2773 |
0.037848904 |
0.9784102 |
| 106 |
RNY4P34 |
-3.3733e-06 |
1.8026e-06 |
-1.8714 |
0.080923296 |
0.9784102 |
| 84 |
AFF1 |
4.0322e-06 |
2.1918e-06 |
1.8396 |
0.085697477 |
0.9784102 |
| 72 |
GPR155 |
-3.0475e-06 |
1.7681e-06 |
-1.7235 |
0.105335663 |
0.9784102 |
| 113 |
TRIM26 |
-3.1203e-06 |
1.8195e-06 |
-1.7150 |
0.106928741 |
0.9784102 |
| 26 |
CCND3 |
-2.6477e-06 |
1.5666e-06 |
-1.6901 |
0.111678367 |
0.9784102 |
| 85 |
MYD88 |
4.2295e-06 |
2.5028e-06 |
1.6900 |
0.111706778 |
0.9784102 |
| 61 |
MVB12A |
-3.1735e-06 |
1.8911e-06 |
-1.6781 |
0.114026753 |
0.9784102 |
| 9 |
CHMP5 |
5.4749e-06 |
3.4212e-06 |
1.6003 |
0.130377932 |
0.9784102 |
| 105 |
TMEM229B |
-3.4447e-06 |
2.2731e-06 |
-1.5154 |
0.150457288 |
0.9784102 |
| 34 |
KIAA1217 |
-1.2459e-06 |
8.4820e-07 |
-1.4688 |
0.162532511 |
0.9784102 |
| 65 |
MOV10 |
-1.8118e-06 |
1.3541e-06 |
-1.3380 |
0.200838528 |
0.9784102 |
| 79 |
LGALS9 |
-3.0486e-06 |
2.3050e-06 |
-1.3226 |
0.205776781 |
0.9784102 |
| 58 |
SCARB2 |
2.3239e-06 |
1.7767e-06 |
1.3080 |
0.210569468 |
0.9784102 |
| 117 |
RP3.508I15.21 |
-2.9880e-06 |
2.3086e-06 |
-1.2943 |
0.215144121 |
0.9784102 |
| 15 |
MYL12A |
2.4404e-06 |
1.8899e-06 |
1.2913 |
0.216140875 |
0.9784102 |
| 45 |
TRIM22 |
3.4477e-06 |
2.7726e-06 |
1.2435 |
0.232771521 |
0.9784102 |
| 53 |
STX17 |
-8.7470e-07 |
7.2210e-07 |
-1.2112 |
0.244556584 |
0.9784102 |
| 96 |
ANKFY1 |
-1.7091e-06 |
1.4311e-06 |
-1.1942 |
0.250940977 |
0.9784102 |
| 4 |
SLC38A5 |
-2.7131e-06 |
2.3545e-06 |
-1.1523 |
0.267225821 |
0.9784102 |
| 51 |
CHST12 |
-1.7359e-06 |
1.5975e-06 |
-1.0866 |
0.294350779 |
0.9784102 |
| 114 |
APOBEC3G |
2.3236e-06 |
2.1834e-06 |
1.0642 |
0.304060607 |
0.9784102 |
| 75 |
DTX3L |
-2.0650e-06 |
1.9452e-06 |
-1.0616 |
0.305221078 |
0.9784102 |
| 74 |
AIM2 |
3.2349e-06 |
3.0661e-06 |
1.0551 |
0.308090233 |
0.9784102 |
| 41 |
HELB |
-2.4039e-06 |
2.3295e-06 |
-1.0319 |
0.318469673 |
0.9784102 |
| 92 |
UBA7 |
-1.7696e-06 |
1.7173e-06 |
-1.0304 |
0.319138057 |
0.9784102 |
| 13 |
REC8 |
2.3933e-06 |
2.3763e-06 |
1.0071 |
0.329834433 |
0.9784102 |
| 66 |
UBE2L6 |
2.6362e-06 |
2.6227e-06 |
1.0052 |
0.330764136 |
0.9784102 |
| 77 |
SLFN5 |
3.2431e-06 |
3.5031e-06 |
0.9258 |
0.369215229 |
0.9784102 |
| 18 |
PRKD2 |
-1.6626e-06 |
1.8073e-06 |
-0.9199 |
0.372169663 |
0.9784102 |
| 20 |
LGALS3BP |
-1.3853e-06 |
1.5537e-06 |
-0.8916 |
0.386695942 |
0.9784102 |
| 21 |
DHX58 |
1.7813e-06 |
2.0180e-06 |
0.8827 |
0.391330703 |
0.9784102 |
| 3 |
ETV7 |
3.2521e-06 |
3.7676e-06 |
0.8632 |
0.401631887 |
0.9784102 |
| 39 |
RBCK1 |
-1.7221e-06 |
2.0195e-06 |
-0.8527 |
0.407220386 |
0.9784102 |
| 19 |
C1GALT1 |
1.2931e-06 |
1.5583e-06 |
0.8298 |
0.419663460 |
0.9784102 |
| 42 |
APOL2 |
2.6330e-06 |
3.1761e-06 |
0.8290 |
0.420100564 |
0.9784102 |
| 112 |
AC009950.2 |
-3.0621e-06 |
3.7182e-06 |
-0.8235 |
0.423110108 |
0.9784102 |
| 70 |
DBF4B |
-1.7741e-06 |
2.1615e-06 |
-0.8207 |
0.424640836 |
0.9784102 |
| 62 |
IFITM3 |
-3.2773e-06 |
4.0599e-06 |
-0.8072 |
0.432153198 |
0.9784102 |
| 71 |
GBP4 |
2.9504e-06 |
3.7469e-06 |
0.7874 |
0.443290879 |
0.9784102 |
| 94 |
USP18 |
-3.8446e-06 |
5.0005e-06 |
-0.7688 |
0.453918801 |
0.9784102 |
| 32 |
IFIT2 |
2.7442e-06 |
3.7111e-06 |
0.7395 |
0.471041407 |
0.9784102 |
| 43 |
BST2 |
-2.6535e-06 |
3.7922e-06 |
-0.6997 |
0.494807090 |
0.9784102 |
| 82 |
STAT2 |
-1.4173e-06 |
2.0471e-06 |
-0.6923 |
0.499312036 |
0.9784102 |
| 100 |
FANCA |
-1.2527e-06 |
1.8332e-06 |
-0.6834 |
0.504801843 |
0.9784102 |
| 1 |
LAP3 |
-1.7551e-06 |
2.5923e-06 |
-0.6771 |
0.508675322 |
0.9784102 |
| 37 |
ZNFX1 |
-2.0604e-06 |
3.1460e-06 |
-0.6549 |
0.522423491 |
0.9784102 |
| 95 |
IFITM2 |
-2.1620e-06 |
3.3253e-06 |
-0.6502 |
0.525408478 |
0.9784102 |
| 87 |
CNP |
-7.8560e-07 |
1.2109e-06 |
-0.6488 |
0.526290851 |
0.9784102 |
| 46 |
XAF1 |
-2.3243e-06 |
3.5980e-06 |
-0.6460 |
0.528047992 |
0.9784102 |
| 33 |
CD274 |
2.3761e-06 |
3.8925e-06 |
0.6104 |
0.550716176 |
0.9784102 |
| 78 |
TTC21A |
-8.7300e-07 |
1.4427e-06 |
-0.6051 |
0.554151171 |
0.9784102 |
| 81 |
TRIM56 |
-1.0130e-06 |
1.6896e-06 |
-0.5996 |
0.557746348 |
0.9784102 |
| 91 |
PARP10 |
-1.5040e-06 |
2.5737e-06 |
-0.5844 |
0.567647135 |
0.9784102 |
| 28 |
IL18R1 |
6.6870e-07 |
1.1789e-06 |
0.5672 |
0.578978094 |
0.9784102 |
| 12 |
PSME2 |
-1.3640e-06 |
2.4560e-06 |
-0.5554 |
0.586824348 |
0.9784102 |
| 110 |
APOL6 |
9.1320e-07 |
1.6826e-06 |
0.5427 |
0.595293184 |
0.9784102 |
| 116 |
RP11.468E2.4 |
-1.4127e-06 |
2.6595e-06 |
-0.5312 |
0.603071179 |
0.9784102 |
| 22 |
UNC93B1 |
-9.8950e-07 |
1.8829e-06 |
-0.5255 |
0.606905546 |
0.9784102 |
| 49 |
OASL |
1.4809e-06 |
2.8675e-06 |
0.5164 |
0.613074479 |
0.9784102 |
| 104 |
C5orf56 |
1.0472e-06 |
2.0649e-06 |
0.5071 |
0.619428053 |
0.9784102 |
| 83 |
GIMAP8 |
8.6130e-07 |
1.7145e-06 |
0.5024 |
0.622708582 |
0.9784102 |
| 31 |
IFIT3 |
2.7502e-06 |
5.6960e-06 |
0.4828 |
0.636189331 |
0.9784102 |
| 67 |
MX1 |
-2.3317e-06 |
4.8445e-06 |
-0.4813 |
0.637236308 |
0.9784102 |
| 98 |
TRIM69 |
-9.1700e-07 |
1.9863e-06 |
-0.4617 |
0.650955688 |
0.9784102 |
| 57 |
HERC6 |
-1.6512e-06 |
3.5801e-06 |
-0.4612 |
0.651262664 |
0.9784102 |
| 16 |
TNFSF13B |
-1.0552e-06 |
2.3196e-06 |
-0.4549 |
0.655700284 |
0.9784102 |
| 52 |
TANK |
4.6280e-07 |
1.0951e-06 |
0.4226 |
0.678572548 |
0.9784102 |
| 99 |
ISG15 |
-1.9897e-06 |
5.1164e-06 |
-0.3889 |
0.702824378 |
0.9784102 |
| 29 |
FBXO6 |
-1.0422e-06 |
2.7657e-06 |
-0.3768 |
0.711575057 |
0.9784102 |
| 108 |
SAMD9 |
-6.6170e-07 |
1.8261e-06 |
-0.3624 |
0.722130410 |
0.9784102 |
| 40 |
IFI6 |
-2.1696e-06 |
6.1312e-06 |
-0.3539 |
0.728361522 |
0.9784102 |
| 102 |
SPATS2L |
-2.1390e-07 |
6.1170e-07 |
-0.3498 |
0.731381088 |
0.9784102 |
| 6 |
SP100 |
-5.4410e-07 |
1.5630e-06 |
-0.3481 |
0.732612113 |
0.9784102 |
| 103 |
CASP4 |
-5.8400e-07 |
1.7454e-06 |
-0.3346 |
0.742563833 |
0.9784102 |
| 27 |
STAT1 |
7.4490e-07 |
2.3435e-06 |
0.3179 |
0.754965125 |
0.9784102 |
| 36 |
NMI |
4.9110e-07 |
1.6022e-06 |
0.3065 |
0.763419411 |
0.9784102 |
| 2 |
CD38 |
8.4820e-07 |
2.7992e-06 |
0.3030 |
0.766036072 |
0.9784102 |
| 10 |
LAG3 |
-1.1289e-06 |
3.7963e-06 |
-0.2974 |
0.770266807 |
0.9784102 |
| 23 |
OAS3 |
9.9180e-07 |
3.7190e-06 |
0.2667 |
0.793345866 |
0.9784102 |
| 97 |
IFIT1 |
1.2816e-06 |
5.1241e-06 |
0.2501 |
0.805886347 |
0.9784102 |
| 63 |
STOM |
-5.5460e-07 |
2.2855e-06 |
-0.2427 |
0.811561758 |
0.9784102 |
| 30 |
GBP1 |
9.8060e-07 |
4.0482e-06 |
0.2422 |
0.811883750 |
0.9784102 |
| 89 |
SAMD9L |
7.0160e-07 |
2.9882e-06 |
0.2348 |
0.817551119 |
0.9784102 |
| 50 |
SP110 |
4.8750e-07 |
2.1070e-06 |
0.2314 |
0.820155357 |
0.9784102 |
| 14 |
SAMHD1 |
-5.9420e-07 |
2.6938e-06 |
-0.2206 |
0.828403397 |
0.9784102 |
| 76 |
IFI27 |
-5.7200e-07 |
2.5978e-06 |
-0.2202 |
0.828694211 |
0.9784102 |
| 55 |
IFI44L |
-1.3133e-06 |
6.1210e-06 |
-0.2146 |
0.833006194 |
0.9784102 |
| 54 |
DDX60 |
-4.4100e-07 |
2.1145e-06 |
-0.2086 |
0.837591422 |
0.9784102 |
| 73 |
AZI2 |
1.5960e-07 |
7.7360e-07 |
0.2063 |
0.839326357 |
0.9784102 |
| 7 |
IFI35 |
4.9950e-07 |
2.5552e-06 |
0.1955 |
0.847625713 |
0.9784102 |
| 88 |
RNF213 |
4.6010e-07 |
2.4371e-06 |
0.1888 |
0.852797528 |
0.9784102 |
| 68 |
ADAR |
2.0180e-07 |
1.0810e-06 |
0.1867 |
0.854421647 |
0.9784102 |
| 38 |
ZBP1 |
-6.2410e-07 |
3.4306e-06 |
-0.1819 |
0.858087399 |
0.9784102 |
| 44 |
C19orf66 |
-3.1910e-07 |
1.7546e-06 |
-0.1818 |
0.858147129 |
0.9784102 |
| 47 |
ALOX5AP |
3.0180e-07 |
1.6759e-06 |
0.1801 |
0.859476794 |
0.9784102 |
| 115 |
PSMB9 |
-5.4380e-07 |
3.0432e-06 |
-0.1787 |
0.860563274 |
0.9784102 |
| 56 |
IFI44 |
8.4100e-07 |
4.9857e-06 |
0.1687 |
0.868302678 |
0.9784102 |
| 35 |
TNFSF10 |
-3.8940e-07 |
2.3434e-06 |
-0.1662 |
0.870256630 |
0.9784102 |
| 90 |
ODF3B |
-4.5140e-07 |
2.8756e-06 |
-0.1570 |
0.877358650 |
0.9784102 |
| 59 |
PML |
-3.9640e-07 |
2.6247e-06 |
-0.1510 |
0.881971075 |
0.9784102 |
| 69 |
LY6E |
-5.3990e-07 |
3.7327e-06 |
-0.1446 |
0.886922801 |
0.9784102 |
| 8 |
SP140 |
-4.5080e-07 |
3.1182e-06 |
-0.1446 |
0.886963785 |
0.9784102 |
| 111 |
GBP1P1 |
-6.7910e-07 |
4.8186e-06 |
-0.1409 |
0.889797353 |
0.9784102 |
| 48 |
CMPK2 |
4.6970e-07 |
3.7269e-06 |
0.1260 |
0.901388972 |
0.9784102 |
| 17 |
PARP4 |
7.8600e-08 |
6.9290e-07 |
0.1135 |
0.911176290 |
0.9784102 |
| 24 |
OAS2 |
-4.9310e-07 |
4.3628e-06 |
-0.1130 |
0.911510354 |
0.9784102 |
| 86 |
PARP14 |
1.1940e-07 |
2.5983e-06 |
0.0459 |
0.963960516 |
0.9970929 |
| 109 |
IRF9 |
1.1640e-07 |
2.8617e-06 |
0.0407 |
0.968083427 |
0.9970929 |
| 80 |
IRS1 |
-4.5500e-08 |
1.1367e-06 |
-0.0400 |
0.968606948 |
0.9970929 |
| 5 |
TYMP |
-7.0100e-08 |
3.9543e-06 |
-0.0177 |
0.986079935 |
0.9970929 |
| 64 |
GBP5 |
6.0100e-08 |
4.7043e-06 |
0.0128 |
0.989979569 |
0.9970929 |
| 11 |
APOL1 |
-3.0900e-08 |
3.2844e-06 |
-0.0094 |
0.992617645 |
0.9970929 |
| 93 |
MX2 |
-1.8100e-08 |
4.6008e-06 |
-0.0039 |
0.996906239 |
0.9970929 |
| 60 |
NLRC5 |
9.0000e-09 |
2.4308e-06 |
0.0037 |
0.997092893 |
0.9970929 |
gene_FunReg(as.matrix(rlog.isgs.05.1.raw), isgs.rld.lin[,235], "Core ISGs", "Plasma Viral Load")
Top Genes from Core ISGs Associated with Outcome: Plasma Viral Load by p.value (Sample Size = NA)
| 45 |
TMEM229B |
-3.4447e-06 |
2.2731e-06 |
-1.5154 |
0.1504573 |
0.9970929 |
| 52 |
RP3.508I15.21 |
-2.9880e-06 |
2.3086e-06 |
-1.2943 |
0.2151441 |
0.9970929 |
| 20 |
TRIM22 |
3.4477e-06 |
2.7726e-06 |
1.2435 |
0.2327715 |
0.9970929 |
| 49 |
APOBEC3G |
2.3236e-06 |
2.1834e-06 |
1.0642 |
0.3040606 |
0.9970929 |
| 34 |
AIM2 |
3.2349e-06 |
3.0661e-06 |
1.0551 |
0.3080902 |
0.9970929 |
| 30 |
UBE2L6 |
2.6362e-06 |
2.6227e-06 |
1.0052 |
0.3307641 |
0.9970929 |
| 2 |
ETV7 |
3.2521e-06 |
3.7676e-06 |
0.8632 |
0.4016319 |
0.9970929 |
| 48 |
AC009950.2 |
-3.0621e-06 |
3.7182e-06 |
-0.8235 |
0.4231101 |
0.9970929 |
| 28 |
IFITM3 |
-3.2773e-06 |
4.0599e-06 |
-0.8072 |
0.4321532 |
0.9970929 |
| 33 |
GBP4 |
2.9504e-06 |
3.7469e-06 |
0.7874 |
0.4432909 |
0.9970929 |
| 40 |
USP18 |
-3.8446e-06 |
5.0005e-06 |
-0.7688 |
0.4539188 |
0.9970929 |
| 14 |
IFIT2 |
2.7442e-06 |
3.7111e-06 |
0.7395 |
0.4710414 |
0.9970929 |
| 19 |
BST2 |
-2.6535e-06 |
3.7922e-06 |
-0.6997 |
0.4948071 |
0.9970929 |
| 16 |
ZNFX1 |
-2.0604e-06 |
3.1460e-06 |
-0.6549 |
0.5224235 |
0.9970929 |
| 41 |
IFITM2 |
-2.1620e-06 |
3.3253e-06 |
-0.6502 |
0.5254085 |
0.9970929 |
| 21 |
XAF1 |
-2.3243e-06 |
3.5980e-06 |
-0.6460 |
0.5280480 |
0.9970929 |
| 15 |
CD274 |
2.3761e-06 |
3.8925e-06 |
0.6104 |
0.5507162 |
0.9970929 |
| 38 |
PARP10 |
-1.5040e-06 |
2.5737e-06 |
-0.5844 |
0.5676471 |
0.9970929 |
| 7 |
PSME2 |
-1.3640e-06 |
2.4560e-06 |
-0.5554 |
0.5868243 |
0.9970929 |
| 51 |
RP11.468E2.4 |
-1.4127e-06 |
2.6595e-06 |
-0.5312 |
0.6030712 |
0.9970929 |
| 13 |
IFIT3 |
2.7502e-06 |
5.6960e-06 |
0.4828 |
0.6361893 |
0.9970929 |
| 31 |
MX1 |
-2.3317e-06 |
4.8445e-06 |
-0.4813 |
0.6372363 |
0.9970929 |
| 43 |
TRIM69 |
-9.1700e-07 |
1.9863e-06 |
-0.4617 |
0.6509557 |
0.9970929 |
| 25 |
HERC6 |
-1.6512e-06 |
3.5801e-06 |
-0.4612 |
0.6512627 |
0.9970929 |
| 8 |
TNFSF13B |
-1.0552e-06 |
2.3196e-06 |
-0.4549 |
0.6557003 |
0.9970929 |
| 44 |
ISG15 |
-1.9897e-06 |
5.1164e-06 |
-0.3889 |
0.7028244 |
0.9970929 |
| 18 |
IFI6 |
-2.1696e-06 |
6.1312e-06 |
-0.3539 |
0.7283615 |
0.9970929 |
| 11 |
STAT1 |
7.4490e-07 |
2.3435e-06 |
0.3179 |
0.7549651 |
0.9970929 |
| 1 |
CD38 |
8.4820e-07 |
2.7992e-06 |
0.3030 |
0.7660361 |
0.9970929 |
| 5 |
LAG3 |
-1.1289e-06 |
3.7963e-06 |
-0.2974 |
0.7702668 |
0.9970929 |
| 9 |
OAS3 |
9.9180e-07 |
3.7190e-06 |
0.2667 |
0.7933459 |
0.9970929 |
| 42 |
IFIT1 |
1.2816e-06 |
5.1241e-06 |
0.2501 |
0.8058863 |
0.9970929 |
| 12 |
GBP1 |
9.8060e-07 |
4.0482e-06 |
0.2422 |
0.8118837 |
0.9970929 |
| 36 |
SAMD9L |
7.0160e-07 |
2.9882e-06 |
0.2348 |
0.8175511 |
0.9970929 |
| 23 |
IFI44L |
-1.3133e-06 |
6.1210e-06 |
-0.2146 |
0.8330062 |
0.9970929 |
| 17 |
ZBP1 |
-6.2410e-07 |
3.4306e-06 |
-0.1819 |
0.8580874 |
0.9970929 |
| 50 |
PSMB9 |
-5.4380e-07 |
3.0432e-06 |
-0.1787 |
0.8605633 |
0.9970929 |
| 24 |
IFI44 |
8.4100e-07 |
4.9857e-06 |
0.1687 |
0.8683027 |
0.9970929 |
| 37 |
ODF3B |
-4.5140e-07 |
2.8756e-06 |
-0.1570 |
0.8773586 |
0.9970929 |
| 26 |
PML |
-3.9640e-07 |
2.6247e-06 |
-0.1510 |
0.8819711 |
0.9970929 |
| 32 |
LY6E |
-5.3990e-07 |
3.7327e-06 |
-0.1446 |
0.8869228 |
0.9970929 |
| 4 |
SP140 |
-4.5080e-07 |
3.1182e-06 |
-0.1446 |
0.8869638 |
0.9970929 |
| 47 |
GBP1P1 |
-6.7910e-07 |
4.8186e-06 |
-0.1409 |
0.8897974 |
0.9970929 |
| 22 |
CMPK2 |
4.6970e-07 |
3.7269e-06 |
0.1260 |
0.9013890 |
0.9970929 |
| 10 |
OAS2 |
-4.9310e-07 |
4.3628e-06 |
-0.1130 |
0.9115104 |
0.9970929 |
| 35 |
PARP14 |
1.1940e-07 |
2.5983e-06 |
0.0459 |
0.9639605 |
0.9970929 |
| 46 |
IRF9 |
1.1640e-07 |
2.8617e-06 |
0.0407 |
0.9680834 |
0.9970929 |
| 3 |
TYMP |
-7.0100e-08 |
3.9543e-06 |
-0.0177 |
0.9860799 |
0.9970929 |
| 29 |
GBP5 |
6.0100e-08 |
4.7043e-06 |
0.0128 |
0.9899796 |
0.9970929 |
| 6 |
APOL1 |
-3.0900e-08 |
3.2844e-06 |
-0.0094 |
0.9926176 |
0.9970929 |
| 39 |
MX2 |
-1.8100e-08 |
4.6008e-06 |
-0.0039 |
0.9969062 |
0.9970929 |
| 27 |
NLRC5 |
9.0000e-09 |
2.4308e-06 |
0.0037 |
0.9970929 |
0.9970929 |
## betas
gene_FunReg(as.matrix(rlog.genesbeta.05.raw), isgs.rld.lin[,235], "IFN-beta Genes", "Plasma Viral Load")
Top Genes from IFN-beta Genes Associated with Outcome: Plasma Viral Load by p.value (Sample Size = NA)
| 6 |
THOC3 |
8.16970e-06 |
2.1273e-06 |
3.8404 |
0.001604998 |
0.1516918 |
| 21 |
CCNB1IP1 |
4.38260e-06 |
1.2289e-06 |
3.5664 |
0.002813188 |
0.1516918 |
| 91 |
AQP3 |
1.34789e-05 |
4.3732e-06 |
3.0821 |
0.007589009 |
0.1516918 |
| 47 |
ZNF227 |
8.43510e-06 |
2.7846e-06 |
3.0292 |
0.008454548 |
0.1516918 |
| 57 |
CCDC90B |
5.34980e-06 |
1.8182e-06 |
2.9424 |
0.010088503 |
0.1516918 |
| 46 |
TAF4 |
3.26670e-06 |
1.1609e-06 |
2.8139 |
0.013088513 |
0.1516918 |
| 35 |
RPS25 |
7.27780e-06 |
2.6190e-06 |
2.7788 |
0.014047395 |
0.1516918 |
| 4 |
GRN |
-3.55480e-06 |
1.3096e-06 |
-2.7145 |
0.015986286 |
0.1516918 |
| 82 |
SLC35B2 |
9.36520e-06 |
3.5971e-06 |
2.6035 |
0.019957500 |
0.1516918 |
| 18 |
HNRNPH3 |
5.85750e-06 |
2.2539e-06 |
2.5988 |
0.020147286 |
0.1516918 |
| 105 |
C8orf59 |
3.03300e-06 |
1.1766e-06 |
2.5777 |
0.021012088 |
0.1516918 |
| 111 |
CSF1 |
5.06860e-06 |
1.9843e-06 |
2.5544 |
0.022006146 |
0.1516918 |
| 3 |
IFNGR1 |
6.57860e-06 |
2.5888e-06 |
2.5411 |
0.022591048 |
0.1516918 |
| 44 |
SHFM1 |
7.10040e-06 |
2.8023e-06 |
2.5338 |
0.022921277 |
0.1516918 |
| 114 |
GTF2F2 |
3.17900e-06 |
1.2569e-06 |
2.5293 |
0.023125894 |
0.1516918 |
| 23 |
TMEM87A |
7.00950e-06 |
2.8292e-06 |
2.4776 |
0.025612899 |
0.1516918 |
| 130 |
GTF2H5 |
4.82680e-06 |
1.9488e-06 |
2.4768 |
0.025651107 |
0.1516918 |
| 11 |
ARFGEF1 |
3.95820e-06 |
1.6067e-06 |
2.4635 |
0.026333254 |
0.1516918 |
| 34 |
KDM3A |
2.80060e-06 |
1.1438e-06 |
2.4485 |
0.027122151 |
0.1516918 |
| 9 |
ATG5 |
5.19560e-06 |
2.1300e-06 |
2.4392 |
0.027620701 |
0.1516918 |
| 85 |
BSDC1 |
4.14290e-06 |
1.7033e-06 |
2.4323 |
0.027999339 |
0.1516918 |
| 22 |
POFUT1 |
4.12320e-06 |
1.6996e-06 |
2.4260 |
0.028346229 |
0.1516918 |
| 70 |
EBAG9 |
1.35210e-06 |
5.6920e-07 |
2.3755 |
0.031283332 |
0.1516918 |
| 62 |
KIF21A |
3.53700e-06 |
1.4958e-06 |
2.3647 |
0.031950968 |
0.1516918 |
| 117 |
UCKL1 |
7.11860e-06 |
3.0321e-06 |
2.3478 |
0.033020643 |
0.1516918 |
| 75 |
TCEB1 |
4.09510e-06 |
1.7516e-06 |
2.3379 |
0.033662550 |
0.1516918 |
| 37 |
PROSER1 |
5.39580e-06 |
2.3235e-06 |
2.3223 |
0.034695553 |
0.1516918 |
| 101 |
C16orf91 |
7.46410e-06 |
3.2224e-06 |
2.3164 |
0.035096214 |
0.1516918 |
| 83 |
UBR1 |
3.58950e-06 |
1.5804e-06 |
2.2712 |
0.038293995 |
0.1516918 |
| 104 |
EIF1AD |
6.78850e-06 |
3.0307e-06 |
2.2399 |
0.040670109 |
0.1516918 |
| 39 |
B4GALT4 |
8.30830e-06 |
3.7523e-06 |
2.2142 |
0.042722876 |
0.1516918 |
| 49 |
SEC61G |
8.97380e-06 |
4.0636e-06 |
2.2084 |
0.043200591 |
0.1516918 |
| 1 |
RANBP9 |
4.45960e-06 |
2.0199e-06 |
2.2078 |
0.043247731 |
0.1516918 |
| 96 |
NUDT21 |
6.87410e-06 |
3.1310e-06 |
2.1955 |
0.044276264 |
0.1516918 |
| 51 |
CYP2J2 |
6.23680e-06 |
2.8448e-06 |
2.1923 |
0.044543195 |
0.1516918 |
| 67 |
SRP9 |
7.85510e-06 |
3.6170e-06 |
2.1717 |
0.046325242 |
0.1516918 |
| 64 |
SMAD4 |
4.08460e-06 |
1.9064e-06 |
2.1426 |
0.048958866 |
0.1516918 |
| 90 |
KIAA0196 |
4.05850e-06 |
1.9210e-06 |
2.1127 |
0.051797504 |
0.1516918 |
| 89 |
SUN1 |
6.98530e-06 |
3.3226e-06 |
2.1023 |
0.052824245 |
0.1516918 |
| 88 |
FBXO8 |
4.55440e-06 |
2.1704e-06 |
2.0984 |
0.053215036 |
0.1516918 |
| 60 |
NUP54 |
2.90160e-06 |
1.4079e-06 |
2.0609 |
0.057094532 |
0.1516918 |
| 30 |
SMAP1 |
4.08070e-06 |
1.9852e-06 |
2.0556 |
0.057658829 |
0.1516918 |
| 29 |
RWDD1 |
4.69750e-06 |
2.3057e-06 |
2.0374 |
0.059656236 |
0.1516918 |
| 36 |
MYL12B |
5.06790e-06 |
2.4882e-06 |
2.0368 |
0.059723424 |
0.1516918 |
| 99 |
MUS81 |
5.27190e-06 |
2.6010e-06 |
2.0269 |
0.060833835 |
0.1516918 |
| 113 |
ZBTB6 |
3.34140e-06 |
1.6537e-06 |
2.0205 |
0.061553313 |
0.1516918 |
| 81 |
DSCR3 |
3.82740e-06 |
1.9049e-06 |
2.0092 |
0.062859198 |
0.1516918 |
| 10 |
ALDH18A1 |
7.13270e-06 |
3.5609e-06 |
2.0031 |
0.063581362 |
0.1516918 |
| 61 |
USO1 |
2.11550e-06 |
1.0595e-06 |
1.9968 |
0.064329048 |
0.1516918 |
| 78 |
FAM126B |
6.30420e-06 |
3.1574e-06 |
1.9967 |
0.064341779 |
0.1516918 |
| 50 |
EMC7 |
5.48180e-06 |
2.7561e-06 |
1.9889 |
0.065268537 |
0.1516918 |
| 65 |
CREG1 |
4.36170e-06 |
2.1969e-06 |
1.9854 |
0.065697339 |
0.1516918 |
| 26 |
NDUFC1 |
6.40980e-06 |
3.2288e-06 |
1.9852 |
0.065723335 |
0.1516918 |
| 92 |
GTF2A1 |
6.11600e-06 |
3.0814e-06 |
1.9848 |
0.065766727 |
0.1516918 |
| 86 |
JAK1 |
1.93230e-06 |
9.7670e-07 |
1.9783 |
0.066560207 |
0.1516918 |
| 54 |
CAB39 |
5.49780e-06 |
2.7880e-06 |
1.9720 |
0.067344155 |
0.1516918 |
| 32 |
SF3B6 |
5.72200e-06 |
2.9031e-06 |
1.9710 |
0.067461820 |
0.1516918 |
| 25 |
EIF4H |
3.02740e-06 |
1.5373e-06 |
1.9693 |
0.067677898 |
0.1516918 |
| 66 |
RFWD2 |
3.72150e-06 |
1.9506e-06 |
1.9079 |
0.075739303 |
0.1666000 |
| 8 |
HPF1 |
5.16820e-06 |
2.7400e-06 |
1.8862 |
0.078781446 |
0.1666000 |
| 123 |
CAPZA2 |
2.46000e-06 |
1.3084e-06 |
1.8802 |
0.079642215 |
0.1666000 |
| 45 |
PSMG2 |
4.46960e-06 |
2.3778e-06 |
1.8797 |
0.079709443 |
0.1666000 |
| 87 |
RPL22L1 |
7.14090e-06 |
3.8132e-06 |
1.8727 |
0.080736912 |
0.1666000 |
| 97 |
GLOD4 |
2.31390e-06 |
1.2466e-06 |
1.8561 |
0.083185326 |
0.1689702 |
| 68 |
CALM2 |
4.46570e-06 |
2.4631e-06 |
1.8130 |
0.089883328 |
0.1797667 |
| 41 |
EBPL |
2.84730e-06 |
1.5876e-06 |
1.7935 |
0.093077858 |
0.1833352 |
| 63 |
DCAF5 |
3.62870e-06 |
2.0518e-06 |
1.7685 |
0.097295614 |
0.1887825 |
| 95 |
CUL5 |
2.55780e-06 |
1.4569e-06 |
1.7557 |
0.099540731 |
0.1902985 |
| 24 |
DECR1 |
4.27000e-06 |
2.4532e-06 |
1.7406 |
0.102221577 |
0.1925914 |
| 112 |
AP3M1 |
3.38730e-06 |
1.9667e-06 |
1.7223 |
0.105563698 |
0.1960469 |
| 43 |
SLC10A3 |
4.18740e-06 |
2.4544e-06 |
1.7061 |
0.108600395 |
0.1968852 |
| 77 |
PTPRN2 |
4.59840e-06 |
2.6989e-06 |
1.7038 |
0.109044126 |
0.1968852 |
| 58 |
ADAM10 |
2.83980e-06 |
1.6898e-06 |
1.6806 |
0.113545975 |
0.2002060 |
| 124 |
TRIQK |
3.50970e-06 |
2.1003e-06 |
1.6711 |
0.115428677 |
0.2002060 |
| 121 |
FOXJ3 |
4.96330e-06 |
2.9708e-06 |
1.6707 |
0.115503445 |
0.2002060 |
| 73 |
BAG3 |
5.08620e-06 |
3.0723e-06 |
1.6555 |
0.118590878 |
0.2023011 |
| 14 |
TSG101 |
3.13600e-06 |
1.9072e-06 |
1.6443 |
0.120902234 |
0.2023011 |
| 27 |
GTF2H1 |
2.99150e-06 |
1.8218e-06 |
1.6420 |
0.121380654 |
0.2023011 |
| 84 |
EFCAB14 |
2.98850e-06 |
1.8530e-06 |
1.6128 |
0.127631633 |
0.2073992 |
| 56 |
HS6ST1 |
4.42760e-06 |
2.7564e-06 |
1.6063 |
0.129054179 |
0.2073992 |
| 94 |
CCT2 |
3.25670e-06 |
2.0304e-06 |
1.6040 |
0.129567729 |
0.2073992 |
| 16 |
AK6 |
4.02520e-06 |
2.5448e-06 |
1.5817 |
0.134565504 |
0.2073992 |
| 116 |
S100A10 |
3.44730e-06 |
2.1808e-06 |
1.5807 |
0.134793224 |
0.2073992 |
| 15 |
UBE2A |
4.47820e-06 |
2.8346e-06 |
1.5798 |
0.134995916 |
0.2073992 |
| 109 |
X15.Sep |
4.56290e-06 |
2.8931e-06 |
1.5772 |
0.135607185 |
0.2073992 |
| 126 |
PPP1CB |
3.03230e-06 |
1.9932e-06 |
1.5213 |
0.148978935 |
0.2252007 |
| 125 |
HLA.A |
2.59910e-06 |
1.7216e-06 |
1.5097 |
0.151891337 |
0.2269641 |
| 13 |
AFF4 |
1.77720e-06 |
1.1859e-06 |
1.4986 |
0.154726933 |
0.2273490 |
| 53 |
DHX9 |
1.59860e-06 |
1.0713e-06 |
1.4922 |
0.156368026 |
0.2273490 |
| 20 |
TIMM9 |
2.07130e-06 |
1.3917e-06 |
1.4883 |
0.157395486 |
0.2273490 |
| 2 |
DERA |
5.47730e-06 |
3.7479e-06 |
1.4614 |
0.164530978 |
0.2326801 |
| 71 |
PTS |
4.16260e-06 |
2.8493e-06 |
1.4609 |
0.164665948 |
0.2326801 |
| 33 |
UNC50 |
3.17820e-06 |
2.2177e-06 |
1.4331 |
0.172337829 |
0.2409023 |
| 69 |
OCIAD2 |
4.39500e-06 |
3.0966e-06 |
1.4193 |
0.176258392 |
0.2437616 |
| 7 |
TAB2 |
2.00410e-06 |
1.4296e-06 |
1.4018 |
0.181323520 |
0.2481269 |
| 98 |
PDCD6IP |
2.56370e-06 |
1.8498e-06 |
1.3859 |
0.186034860 |
0.2519222 |
| 59 |
GTF2B |
2.21940e-06 |
1.6328e-06 |
1.3593 |
0.194145858 |
0.2601955 |
| 129 |
INAFM2 |
4.53300e-06 |
3.3531e-06 |
1.3519 |
0.196450913 |
0.2605981 |
| 17 |
SLC25A24 |
2.78980e-06 |
2.3062e-06 |
1.2097 |
0.245124759 |
0.3187655 |
| 52 |
RNASEL |
1.34790e-06 |
1.1185e-06 |
1.2051 |
0.246827220 |
0.3187655 |
| 5 |
YTHDC2 |
1.89060e-06 |
1.5717e-06 |
1.2029 |
0.247656249 |
0.3187655 |
| 106 |
FAM91A1 |
2.83560e-06 |
2.4189e-06 |
1.1722 |
0.259384060 |
0.3305875 |
| 103 |
ZNF654 |
1.15670e-06 |
1.0566e-06 |
1.0947 |
0.290895239 |
0.3671493 |
| 107 |
SIAH2 |
3.04190e-06 |
2.8714e-06 |
1.0594 |
0.306177516 |
0.3812664 |
| 19 |
ASCC2 |
1.24790e-06 |
1.1824e-06 |
1.0554 |
0.307945913 |
0.3812664 |
| 48 |
VIMP |
1.59470e-06 |
1.5866e-06 |
1.0051 |
0.330788227 |
0.4056837 |
| 119 |
TXNRD1 |
1.22950e-06 |
1.2613e-06 |
0.9748 |
0.345115688 |
0.4192994 |
| 79 |
FAM161B |
1.10630e-06 |
1.1586e-06 |
0.9549 |
0.354762226 |
0.4270286 |
| 76 |
ATP5J |
1.51480e-06 |
1.6082e-06 |
0.9419 |
0.361167328 |
0.4307500 |
| 110 |
SH2D1A |
2.33770e-06 |
2.5215e-06 |
0.9271 |
0.368549633 |
0.4355587 |
| 80 |
MFSD14A |
1.94500e-06 |
2.1432e-06 |
0.9075 |
0.378495518 |
0.4432830 |
| 108 |
FAM89A |
1.45810e-06 |
1.6280e-06 |
0.8956 |
0.384608672 |
0.4464208 |
| 42 |
FAM78A |
-1.41850e-06 |
1.7598e-06 |
-0.8061 |
0.432794767 |
0.4979055 |
| 38 |
ELF1 |
-5.36500e-07 |
7.1280e-07 |
-0.7528 |
0.463240730 |
0.5282570 |
| 55 |
SCYL2 |
7.52200e-07 |
1.0533e-06 |
0.7141 |
0.486120592 |
0.5495276 |
| 100 |
OXSR1 |
1.03510e-06 |
1.6173e-06 |
0.6400 |
0.531804200 |
0.5959875 |
| 74 |
CEBPG |
-5.07000e-07 |
8.7570e-07 |
-0.5789 |
0.571234188 |
0.6347047 |
| 127 |
IFNG.AS1 |
-8.24800e-07 |
1.5321e-06 |
-0.5383 |
0.598237610 |
0.6548766 |
| 72 |
PARP8 |
-5.16700e-07 |
9.6310e-07 |
-0.5365 |
0.599463980 |
0.6548766 |
| 128 |
KIAA1147 |
6.69900e-07 |
1.3276e-06 |
0.5046 |
0.621139124 |
0.6729007 |
| 12 |
CLEC2D |
7.10000e-07 |
1.5964e-06 |
0.4447 |
0.662856197 |
0.7090748 |
| 120 |
TTC37 |
3.76900e-07 |
8.5440e-07 |
0.4411 |
0.665439455 |
0.7090748 |
| 118 |
GFPT1 |
4.14400e-07 |
1.0089e-06 |
0.4108 |
0.687020650 |
0.7212203 |
| 31 |
EPB41L5 |
6.98300e-07 |
1.7204e-06 |
0.4059 |
0.690571913 |
0.7212203 |
| 122 |
SFMBT2 |
6.38600e-07 |
1.5893e-06 |
0.4018 |
0.693481055 |
0.7212203 |
| 40 |
KHDRBS1 |
2.29900e-07 |
8.9040e-07 |
0.2582 |
0.799739716 |
0.8211070 |
| 115 |
PPTC7 |
3.60900e-07 |
1.4152e-06 |
0.2550 |
0.802158380 |
0.8211070 |
| 102 |
GPR171 |
6.20000e-08 |
1.6431e-06 |
0.0377 |
0.970390054 |
0.9779409 |
| 93 |
MICU2 |
3.21000e-08 |
8.5110e-07 |
0.0377 |
0.970418277 |
0.9779409 |
| 28 |
C2CD5 |
3.64000e-08 |
1.3149e-06 |
0.0277 |
0.978264119 |
0.9782641 |
gene_FunReg(as.matrix(rlog.genesbeta.05.1.raw), isgs.rld.lin[,235], "IFN-beta Genes", "Plasma Viral Load")
Top Genes from IFN-beta Genes Associated with Outcome: Plasma Viral Load by p.value (Sample Size = NA)
| 1 |
THOC3 |
8.16970e-06 |
2.1273e-06 |
3.8404 |
0.001604998 |
0.01283998 |
| 4 |
AQP3 |
1.34789e-05 |
4.3732e-06 |
3.0821 |
0.007589009 |
0.03035604 |
| 3 |
SLC35B2 |
9.36520e-06 |
3.5971e-06 |
2.6035 |
0.019957500 |
0.05322000 |
| 5 |
C16orf91 |
7.46410e-06 |
3.2224e-06 |
2.3164 |
0.035096214 |
0.06835660 |
| 2 |
B4GALT4 |
8.30830e-06 |
3.7523e-06 |
2.2142 |
0.042722876 |
0.06835660 |
| 7 |
SH2D1A |
2.33770e-06 |
2.5215e-06 |
0.9271 |
0.368549633 |
0.49139951 |
| 8 |
IFNG.AS1 |
-8.24800e-07 |
1.5321e-06 |
-0.5383 |
0.598237610 |
0.68370013 |
| 6 |
GPR171 |
6.20000e-08 |
1.6431e-06 |
0.0377 |
0.970390054 |
0.97039005 |
isgs.rld.lin[,235] == genesbeta.rld.lin[,428]
## [1] NA NA NA NA NA NA NA NA NA NA NA NA NA TRUE
## [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [29] TRUE TRUE TRUE TRUE
################# CD4 Counts #################
## whole isgs
gene_FunReg(as.matrix(rlog.isgs.05.raw), isgs.rld.lin[,234], "Core ISGs", "CD4 Counts")
Top Genes from Core ISGs Associated with Outcome: CD4 Counts by p.value (Sample Size = -18801)
| 80 |
IRS1 |
0.0007610715 |
0.0001482952 |
5.1321 |
1.932496e-05 |
0.002261021 |
| 61 |
MVB12A |
-0.0010835714 |
0.0002476611 |
-4.3752 |
1.525605e-04 |
0.008924791 |
| 90 |
ODF3B |
-0.0015686938 |
0.0004039165 |
-3.8837 |
5.734632e-04 |
0.015153149 |
| 20 |
LGALS3BP |
-0.0007490935 |
0.0001939187 |
-3.8629 |
6.061176e-04 |
0.015153149 |
| 92 |
UBA7 |
-0.0010256825 |
0.0002672392 |
-3.8381 |
6.475705e-04 |
0.015153149 |
| 85 |
MYD88 |
0.0012700210 |
0.0003375633 |
3.7623 |
7.917648e-04 |
0.015439414 |
| 10 |
LAG3 |
-0.0022022688 |
0.0006142794 |
-3.5851 |
1.262499e-03 |
0.021035242 |
| 107 |
ASAH2B |
0.0014553747 |
0.0004129725 |
3.5241 |
1.480444e-03 |
0.021035242 |
| 101 |
TDRD7 |
0.0017143951 |
0.0004915349 |
3.4878 |
1.627094e-03 |
0.021035242 |
| 112 |
AC009950.2 |
-0.0018182819 |
0.0005287117 |
-3.4391 |
1.846379e-03 |
0.021035242 |
| 19 |
C1GALT1 |
0.0006697419 |
0.0001962611 |
3.4125 |
1.977672e-03 |
0.021035242 |
| 65 |
MOV10 |
-0.0006626383 |
0.0001967015 |
-3.3688 |
2.213713e-03 |
0.021583705 |
| 22 |
UNC93B1 |
-0.0009141223 |
0.0002743428 |
-3.3320 |
2.432518e-03 |
0.021892666 |
| 115 |
PSMB9 |
-0.0017736404 |
0.0005453889 |
-3.2521 |
2.983743e-03 |
0.024635716 |
| 12 |
PSME2 |
-0.0011765994 |
0.0003643089 |
-3.2297 |
3.158425e-03 |
0.024635716 |
| 84 |
AFF1 |
0.0011163424 |
0.0003504499 |
3.1855 |
3.532698e-03 |
0.025832855 |
| 60 |
NLRC5 |
-0.0014858749 |
0.0004831703 |
-3.0753 |
4.659137e-03 |
0.032065824 |
| 87 |
CNP |
-0.0006228970 |
0.0002043938 |
-3.0475 |
4.992483e-03 |
0.032451141 |
| 98 |
TRIM69 |
-0.0010965476 |
0.0003655343 |
-2.9998 |
5.619499e-03 |
0.033679603 |
| 18 |
PRKD2 |
-0.0007526942 |
0.0002529494 |
-2.9757 |
5.965341e-03 |
0.033679603 |
| 26 |
CCND3 |
-0.0006605088 |
0.0002224638 |
-2.9691 |
6.063350e-03 |
0.033679603 |
| 105 |
TMEM229B |
-0.0011605751 |
0.0003957111 |
-2.9329 |
6.627422e-03 |
0.033679603 |
| 117 |
RP3.508I15.21 |
-0.0010991850 |
0.0003755405 |
-2.9269 |
6.724723e-03 |
0.033679603 |
| 99 |
ISG15 |
-0.0022389112 |
0.0007678216 |
-2.9159 |
6.908636e-03 |
0.033679603 |
| 17 |
PARP4 |
0.0004448793 |
0.0001542342 |
2.8844 |
7.460929e-03 |
0.034249972 |
| 51 |
CHST12 |
-0.0007499669 |
0.0002607437 |
-2.8763 |
7.611105e-03 |
0.034249972 |
| 113 |
TRIM26 |
-0.0007458627 |
0.0002620257 |
-2.8465 |
8.181397e-03 |
0.035452721 |
| 4 |
SLC38A5 |
-0.0009863791 |
0.0003573311 |
-2.7604 |
1.006865e-02 |
0.042072593 |
| 9 |
CHMP5 |
0.0013876928 |
0.0005075771 |
2.7340 |
1.072590e-02 |
0.042593864 |
| 5 |
TYMP |
-0.0018290393 |
0.0006708685 |
-2.7264 |
1.092150e-02 |
0.042593864 |
| 52 |
TANK |
0.0004418309 |
0.0001637848 |
2.6976 |
1.169407e-02 |
0.044135701 |
| 81 |
TRIM56 |
-0.0006656211 |
0.0002493138 |
-2.6698 |
1.249017e-02 |
0.045036468 |
| 15 |
MYL12A |
0.0008372688 |
0.0003144472 |
2.6627 |
1.270259e-02 |
0.045036468 |
| 37 |
ZNFX1 |
-0.0011380574 |
0.0004322759 |
-2.6327 |
1.363073e-02 |
0.045993842 |
| 79 |
LGALS9 |
-0.0008269940 |
0.0003146165 |
-2.6286 |
1.376361e-02 |
0.045993842 |
| 47 |
ALOX5AP |
-0.0006109527 |
0.0002334813 |
-2.6167 |
1.415195e-02 |
0.045993842 |
| 91 |
PARP10 |
-0.0012017546 |
0.0004682792 |
-2.5663 |
1.591682e-02 |
0.049659253 |
| 75 |
DTX3L |
-0.0007715865 |
0.0003028539 |
-2.5477 |
1.661839e-02 |
0.049659253 |
| 82 |
STAT2 |
-0.0007711986 |
0.0003029924 |
-2.5453 |
1.671270e-02 |
0.049659253 |
| 95 |
IFITM2 |
-0.0011643989 |
0.0004587001 |
-2.5385 |
1.697752e-02 |
0.049659253 |
| 111 |
GBP1P1 |
-0.0019834924 |
0.0007890704 |
-2.5137 |
1.797554e-02 |
0.051296066 |
| 8 |
SP140 |
-0.0012043479 |
0.0004818170 |
-2.4996 |
1.856813e-02 |
0.051725507 |
| 11 |
APOL1 |
-0.0012276064 |
0.0004965735 |
-2.4722 |
1.977233e-02 |
0.053799132 |
| 116 |
RP11.468E2.4 |
-0.0012305421 |
0.0005064644 |
-2.4297 |
2.177894e-02 |
0.057912190 |
| 109 |
IRF9 |
-0.0013114588 |
0.0005462964 |
-2.4006 |
2.325603e-02 |
0.060465674 |
| 58 |
SCARB2 |
0.0006480421 |
0.0002729194 |
2.3745 |
2.466445e-02 |
0.061979475 |
| 46 |
XAF1 |
-0.0013356020 |
0.0005634782 |
-2.3703 |
2.489774e-02 |
0.061979475 |
| 40 |
IFI6 |
-0.0020600915 |
0.0008773353 |
-2.3481 |
2.616220e-02 |
0.063770371 |
| 73 |
AZI2 |
0.0003076636 |
0.0001329935 |
2.3134 |
2.826334e-02 |
0.067485936 |
| 1 |
LAP3 |
-0.0008583774 |
0.0003728348 |
-2.3023 |
2.896444e-02 |
0.067776789 |
| 59 |
PML |
-0.0009161003 |
0.0004000079 |
-2.2902 |
2.974817e-02 |
0.068245794 |
| 64 |
GBP5 |
-0.0017522554 |
0.0007691946 |
-2.2780 |
3.055587e-02 |
0.068677535 |
| 62 |
IFITM3 |
-0.0013126885 |
0.0005792681 |
-2.2661 |
3.136666e-02 |
0.068677535 |
| 78 |
TTC21A |
-0.0006297596 |
0.0002784904 |
-2.2613 |
3.169732e-02 |
0.068677535 |
| 53 |
STX17 |
-0.0002800037 |
0.0001271598 |
-2.2020 |
3.607044e-02 |
0.076731669 |
| 43 |
BST2 |
-0.0012477134 |
0.0005739157 |
-2.1740 |
3.831165e-02 |
0.080043977 |
| 96 |
ANKFY1 |
-0.0004304835 |
0.0001989244 |
-2.1641 |
3.914175e-02 |
0.080343589 |
| 7 |
IFI35 |
-0.0007241745 |
0.0003418864 |
-2.1182 |
4.316883e-02 |
0.085313046 |
| 88 |
RNF213 |
-0.0007705242 |
0.0003644015 |
-2.1145 |
4.350727e-02 |
0.085313046 |
| 27 |
STAT1 |
-0.0008216114 |
0.0003890452 |
-2.1119 |
4.375028e-02 |
0.085313046 |
| 86 |
PARP14 |
-0.0008285693 |
0.0003940227 |
-2.1028 |
4.459394e-02 |
0.085532646 |
| 67 |
MX1 |
-0.0016062367 |
0.0007677195 |
-2.0922 |
4.560670e-02 |
0.086064254 |
| 16 |
TNFSF13B |
-0.0008091647 |
0.0003901229 |
-2.0741 |
4.737746e-02 |
0.087986720 |
| 14 |
SAMHD1 |
-0.0007488932 |
0.0003637907 |
-2.0586 |
4.894751e-02 |
0.089482169 |
| 35 |
TNFSF10 |
-0.0006528738 |
0.0003184832 |
-2.0499 |
4.983944e-02 |
0.089710985 |
| 24 |
OAS2 |
-0.0013845240 |
0.0006792521 |
-2.0383 |
5.106444e-02 |
0.090523332 |
| 39 |
RBCK1 |
-0.0006773025 |
0.0003339869 |
-2.0279 |
5.217865e-02 |
0.091117949 |
| 30 |
GBP1 |
-0.0013166857 |
0.0006578202 |
-2.0016 |
5.510425e-02 |
0.094811720 |
| 72 |
GPR155 |
-0.0006551093 |
0.0003369670 |
-1.9441 |
6.198925e-02 |
0.103731039 |
| 29 |
FBXO6 |
-0.0007765893 |
0.0003997361 |
-1.9428 |
6.216346e-02 |
0.103731039 |
| 69 |
LY6E |
-0.0011344815 |
0.0005858161 |
-1.9366 |
6.294790e-02 |
0.103731039 |
| 70 |
DBF4B |
-0.0006437485 |
0.0003467951 |
-1.8563 |
7.396595e-02 |
0.119922747 |
| 13 |
REC8 |
-0.0006815416 |
0.0003695830 |
-1.8441 |
7.577723e-02 |
0.119922747 |
| 103 |
CASP4 |
-0.0004499502 |
0.0002448097 |
-1.8380 |
7.670086e-02 |
0.119922747 |
| 94 |
USP18 |
-0.0013205160 |
0.0007189137 |
-1.8368 |
7.687356e-02 |
0.119922747 |
| 2 |
CD38 |
-0.0008002076 |
0.0004381767 |
-1.8262 |
7.849846e-02 |
0.120846311 |
| 41 |
HELB |
-0.0006320468 |
0.0003479417 |
-1.8165 |
8.000962e-02 |
0.121320731 |
| 83 |
GIMAP8 |
-0.0004810982 |
0.0002656509 |
-1.8110 |
8.088049e-02 |
0.121320731 |
| 55 |
IFI44L |
-0.0017371281 |
0.0009961360 |
-1.7439 |
9.215368e-02 |
0.134395850 |
| 21 |
DHX58 |
-0.0005475066 |
0.0003143600 |
-1.7417 |
9.254652e-02 |
0.134395850 |
| 44 |
C19orf66 |
-0.0005726334 |
0.0003293135 |
-1.7389 |
9.304328e-02 |
0.134395850 |
| 100 |
FANCA |
-0.0004993951 |
0.0002967748 |
-1.6827 |
1.035454e-01 |
0.145981352 |
| 31 |
IFIT3 |
-0.0014041452 |
0.0008374730 |
-1.6766 |
1.047436e-01 |
0.145981352 |
| 71 |
GBP4 |
-0.0010553067 |
0.0006295364 |
-1.6763 |
1.048071e-01 |
0.145981352 |
| 63 |
STOM |
-0.0006184140 |
0.0003747379 |
-1.6503 |
1.100651e-01 |
0.151501375 |
| 76 |
IFI27 |
-0.0006615508 |
0.0004042347 |
-1.6366 |
1.129168e-01 |
0.153619317 |
| 48 |
CMPK2 |
-0.0009360359 |
0.0005795471 |
-1.6151 |
1.174995e-01 |
0.158016508 |
| 57 |
HERC6 |
-0.0007946757 |
0.0004957958 |
-1.6028 |
1.201952e-01 |
0.159804969 |
| 54 |
DDX60 |
-0.0005266962 |
0.0003342625 |
-1.5757 |
1.263285e-01 |
0.166072338 |
| 74 |
AIM2 |
-0.0008317045 |
0.0005311319 |
-1.5659 |
1.286030e-01 |
0.167183879 |
| 36 |
NMI |
-0.0003771831 |
0.0002512363 |
-1.5013 |
1.444698e-01 |
0.185746847 |
| 25 |
TRIM38 |
-0.0002753587 |
0.0001842454 |
-1.4945 |
1.462249e-01 |
0.185959929 |
| 50 |
SP110 |
-0.0005008878 |
0.0003373691 |
-1.4847 |
1.487985e-01 |
0.187198079 |
| 102 |
SPATS2L |
0.0001866083 |
0.0001283039 |
1.4544 |
1.569479e-01 |
0.195350063 |
| 110 |
APOL6 |
-0.0003971945 |
0.0002837236 |
-1.3999 |
1.725161e-01 |
0.212467144 |
| 106 |
RNY4P34 |
-0.0004467537 |
0.0003291947 |
-1.3571 |
1.855859e-01 |
0.226182785 |
| 23 |
OAS3 |
-0.0007388047 |
0.0006031963 |
-1.2248 |
2.308491e-01 |
0.278446912 |
| 68 |
ADAR |
-0.0002123488 |
0.0001765533 |
-1.2027 |
2.391468e-01 |
0.281969078 |
| 93 |
MX2 |
-0.0007961528 |
0.0006619744 |
-1.2027 |
2.391665e-01 |
0.281969078 |
| 6 |
SP100 |
-0.0002806605 |
0.0002342943 |
-1.1979 |
2.409992e-01 |
0.281969078 |
| 56 |
IFI44 |
-0.0008705497 |
0.0007393347 |
-1.1775 |
2.489171e-01 |
0.288349484 |
| 38 |
ZBP1 |
-0.0005711729 |
0.0004971689 |
-1.1489 |
2.603374e-01 |
0.298622339 |
| 89 |
SAMD9L |
-0.0005163570 |
0.0004747990 |
-1.0875 |
2.860769e-01 |
0.324961138 |
| 114 |
APOBEC3G |
-0.0004163575 |
0.0003917897 |
-1.0627 |
2.969951e-01 |
0.331593013 |
| 66 |
UBE2L6 |
-0.0004551060 |
0.0004287841 |
-1.0614 |
2.975835e-01 |
0.331593013 |
| 3 |
ETV7 |
-0.0005754739 |
0.0005461695 |
-1.0537 |
3.010491e-01 |
0.332290005 |
| 97 |
IFIT1 |
-0.0006999014 |
0.0007681111 |
-0.9112 |
3.699693e-01 |
0.404545902 |
| 108 |
SAMD9 |
-0.0002779836 |
0.0003126883 |
-0.8890 |
3.815710e-01 |
0.413368596 |
| 77 |
SLFN5 |
-0.0004263116 |
0.0004879869 |
-0.8736 |
3.897604e-01 |
0.416956862 |
| 33 |
CD274 |
-0.0004819840 |
0.0005543755 |
-0.8694 |
3.920107e-01 |
0.416956862 |
| 49 |
OASL |
-0.0003461253 |
0.0004436228 |
-0.7802 |
4.418050e-01 |
0.465686396 |
| 45 |
TRIM22 |
-0.0003274848 |
0.0004712422 |
-0.6949 |
4.928203e-01 |
0.514821253 |
| 32 |
IFIT2 |
-0.0002721925 |
0.0005417605 |
-0.5024 |
6.192993e-01 |
0.641221412 |
| 104 |
C5orf56 |
-0.0001604796 |
0.0003261495 |
-0.4920 |
6.265246e-01 |
0.643012077 |
| 42 |
APOL2 |
-0.0001970901 |
0.0004190840 |
-0.4703 |
6.417921e-01 |
0.652953683 |
| 28 |
IL18R1 |
-0.0000709687 |
0.0002320564 |
-0.3058 |
7.620000e-01 |
0.762027910 |
| 34 |
KIAA1217 |
0.0000539773 |
0.0001765185 |
0.3058 |
7.620279e-01 |
0.762027910 |
gene_FunReg(as.matrix(rlog.isgs.05.1.raw), isgs.rld.lin[,234], "Core ISGs", "CD4 Counts")
Top Genes from Core ISGs Associated with Outcome: CD4 Counts by p.value (Sample Size = -18801)
| 37 |
ODF3B |
-0.0015686938 |
0.0004039165 |
-3.8837 |
0.0005734632 |
0.02982008 |
| 5 |
LAG3 |
-0.0022022688 |
0.0006142794 |
-3.5851 |
0.0012624993 |
0.03200391 |
| 48 |
AC009950.2 |
-0.0018182819 |
0.0005287117 |
-3.4391 |
0.0018463792 |
0.03200391 |
| 50 |
PSMB9 |
-0.0017736404 |
0.0005453889 |
-3.2521 |
0.0029837430 |
0.03284762 |
| 7 |
PSME2 |
-0.0011765994 |
0.0003643089 |
-3.2297 |
0.0031584252 |
0.03284762 |
| 27 |
NLRC5 |
-0.0014858749 |
0.0004831703 |
-3.0753 |
0.0046591369 |
0.03592491 |
| 43 |
TRIM69 |
-0.0010965476 |
0.0003655343 |
-2.9998 |
0.0056194994 |
0.03592491 |
| 45 |
TMEM229B |
-0.0011605751 |
0.0003957111 |
-2.9329 |
0.0066274216 |
0.03592491 |
| 52 |
RP3.508I15.21 |
-0.0010991850 |
0.0003755405 |
-2.9269 |
0.0067247229 |
0.03592491 |
| 44 |
ISG15 |
-0.0022389112 |
0.0007678216 |
-2.9159 |
0.0069086364 |
0.03592491 |
| 3 |
TYMP |
-0.0018290393 |
0.0006708685 |
-2.7264 |
0.0109215035 |
0.05162893 |
| 16 |
ZNFX1 |
-0.0011380574 |
0.0004322759 |
-2.6327 |
0.0136307315 |
0.05906650 |
| 38 |
PARP10 |
-0.0012017546 |
0.0004682792 |
-2.5663 |
0.0159168213 |
0.06034642 |
| 41 |
IFITM2 |
-0.0011643989 |
0.0004587001 |
-2.5385 |
0.0169775224 |
0.06034642 |
| 47 |
GBP1P1 |
-0.0019834924 |
0.0007890704 |
-2.5137 |
0.0179755446 |
0.06034642 |
| 4 |
SP140 |
-0.0012043479 |
0.0004818170 |
-2.4996 |
0.0185681305 |
0.06034642 |
| 6 |
APOL1 |
-0.0012276064 |
0.0004965735 |
-2.4722 |
0.0197723305 |
0.06048007 |
| 51 |
RP11.468E2.4 |
-0.0012305421 |
0.0005064644 |
-2.4297 |
0.0217789433 |
0.06291695 |
| 46 |
IRF9 |
-0.0013114588 |
0.0005462964 |
-2.4006 |
0.0232560283 |
0.06364808 |
| 21 |
XAF1 |
-0.0013356020 |
0.0005634782 |
-2.3703 |
0.0248977380 |
0.06473412 |
| 18 |
IFI6 |
-0.0020600915 |
0.0008773353 |
-2.3481 |
0.0261622036 |
0.06478260 |
| 26 |
PML |
-0.0009161003 |
0.0004000079 |
-2.2902 |
0.0297481666 |
0.06796110 |
| 29 |
GBP5 |
-0.0017522554 |
0.0007691946 |
-2.2780 |
0.0305558694 |
0.06796110 |
| 28 |
IFITM3 |
-0.0013126885 |
0.0005792681 |
-2.2661 |
0.0313666626 |
0.06796110 |
| 19 |
BST2 |
-0.0012477134 |
0.0005739157 |
-2.1740 |
0.0383116472 |
0.07968823 |
| 11 |
STAT1 |
-0.0008216114 |
0.0003890452 |
-2.1119 |
0.0437502802 |
0.08469815 |
| 35 |
PARP14 |
-0.0008285693 |
0.0003940227 |
-2.1028 |
0.0445939438 |
0.08469815 |
| 31 |
MX1 |
-0.0016062367 |
0.0007677195 |
-2.0922 |
0.0456066986 |
0.08469815 |
| 8 |
TNFSF13B |
-0.0008091647 |
0.0003901229 |
-2.0741 |
0.0473774647 |
0.08495270 |
| 10 |
OAS2 |
-0.0013845240 |
0.0006792521 |
-2.0383 |
0.0510644439 |
0.08851170 |
| 12 |
GBP1 |
-0.0013166857 |
0.0006578202 |
-2.0016 |
0.0551042473 |
0.09243293 |
| 32 |
LY6E |
-0.0011344815 |
0.0005858161 |
-1.9366 |
0.0629478954 |
0.10229033 |
| 40 |
USP18 |
-0.0013205160 |
0.0007189137 |
-1.8368 |
0.0768735558 |
0.12005647 |
| 1 |
CD38 |
-0.0008002076 |
0.0004381767 |
-1.8262 |
0.0784984582 |
0.12005647 |
| 23 |
IFI44L |
-0.0017371281 |
0.0009961360 |
-1.7439 |
0.0921536814 |
0.13691404 |
| 13 |
IFIT3 |
-0.0014041452 |
0.0008374730 |
-1.6766 |
0.1047436008 |
0.14729650 |
| 33 |
GBP4 |
-0.0010553067 |
0.0006295364 |
-1.6763 |
0.1048071242 |
0.14729650 |
| 22 |
CMPK2 |
-0.0009360359 |
0.0005795471 |
-1.6151 |
0.1174994546 |
0.16026025 |
| 25 |
HERC6 |
-0.0007946757 |
0.0004957958 |
-1.6028 |
0.1201951902 |
0.16026025 |
| 34 |
AIM2 |
-0.0008317045 |
0.0005311319 |
-1.5659 |
0.1286029838 |
0.16718388 |
| 9 |
OAS3 |
-0.0007388047 |
0.0006031963 |
-1.2248 |
0.2308491491 |
0.29278429 |
| 39 |
MX2 |
-0.0007961528 |
0.0006619744 |
-1.2027 |
0.2391665375 |
0.29611095 |
| 24 |
IFI44 |
-0.0008705497 |
0.0007393347 |
-1.1775 |
0.2489170763 |
0.30101600 |
| 17 |
ZBP1 |
-0.0005711729 |
0.0004971689 |
-1.1489 |
0.2603374239 |
0.30767150 |
| 36 |
SAMD9L |
-0.0005163570 |
0.0004747990 |
-1.0875 |
0.2860768992 |
0.32613649 |
| 49 |
APOBEC3G |
-0.0004163575 |
0.0003917897 |
-1.0627 |
0.2969950948 |
0.32613649 |
| 30 |
UBE2L6 |
-0.0004551060 |
0.0004287841 |
-1.0614 |
0.2975834729 |
0.32613649 |
| 2 |
ETV7 |
-0.0005754739 |
0.0005461695 |
-1.0537 |
0.3010490641 |
0.32613649 |
| 42 |
IFIT1 |
-0.0006999014 |
0.0007681111 |
-0.9112 |
0.3699693293 |
0.39262051 |
| 15 |
CD274 |
-0.0004819840 |
0.0005543755 |
-0.8694 |
0.3920107248 |
0.40769115 |
| 20 |
TRIM22 |
-0.0003274848 |
0.0004712422 |
-0.6949 |
0.4928203451 |
0.50248349 |
| 14 |
IFIT2 |
-0.0002721925 |
0.0005417605 |
-0.5024 |
0.6192993121 |
0.61929931 |
## betas
gene_FunReg(as.matrix(rlog.genesbeta.05.raw), isgs.rld.lin[,234], "IFN-beta Genes", "CD4 Counts")
Top Genes from IFN-beta Genes Associated with Outcome: CD4 Counts by p.value (Sample Size = -18801)
| 120 |
TTC37 |
0.0005358599 |
0.0001287513 |
4.1620 |
0.0002717791 |
0.007659695 |
| 111 |
CSF1 |
0.0012696458 |
0.0003114021 |
4.0772 |
0.0003415301 |
0.007659695 |
| 40 |
KHDRBS1 |
0.0005601869 |
0.0001381998 |
4.0535 |
0.0003640346 |
0.007659695 |
| 16 |
AK6 |
0.0014059302 |
0.0003525805 |
3.9875 |
0.0004344734 |
0.007659695 |
| 108 |
FAM89A |
0.0009533171 |
0.0002401430 |
3.9698 |
0.0004556344 |
0.007659695 |
| 99 |
MUS81 |
0.0014277403 |
0.0003748157 |
3.8092 |
0.0006992467 |
0.007659695 |
| 124 |
TRIQK |
0.0011726172 |
0.0003082922 |
3.8036 |
0.0007096999 |
0.007659695 |
| 75 |
TCEB1 |
0.0010812639 |
0.0002848620 |
3.7957 |
0.0007246280 |
0.007659695 |
| 4 |
GRN |
-0.0007831818 |
0.0002065103 |
-3.7925 |
0.0007309762 |
0.007659695 |
| 61 |
USO1 |
0.0006495708 |
0.0001721166 |
3.7740 |
0.0007676093 |
0.007659695 |
| 129 |
INAFM2 |
0.0017077905 |
0.0004622833 |
3.6943 |
0.0009477999 |
0.007659695 |
| 47 |
ZNF227 |
0.0016888185 |
0.0004607800 |
3.6651 |
0.0010233755 |
0.007659695 |
| 60 |
NUP54 |
0.0007504855 |
0.0002054745 |
3.6525 |
0.0010580872 |
0.007659695 |
| 20 |
TIMM9 |
0.0007878312 |
0.0002158457 |
3.6500 |
0.0010649976 |
0.007659695 |
| 117 |
UCKL1 |
0.0016633265 |
0.0004585912 |
3.6270 |
0.0011311535 |
0.007659695 |
| 83 |
UBR1 |
0.0009275473 |
0.0002595275 |
3.5740 |
0.0012998390 |
0.007659695 |
| 63 |
DCAF5 |
0.0011141710 |
0.0003121599 |
3.5692 |
0.0013160971 |
0.007659695 |
| 33 |
UNC50 |
0.0012140825 |
0.0003409622 |
3.5608 |
0.0013455796 |
0.007659695 |
| 104 |
EIF1AD |
0.0017723645 |
0.0004984594 |
3.5557 |
0.0013635173 |
0.007659695 |
| 53 |
DHX9 |
0.0006371057 |
0.0001795923 |
3.5475 |
0.0013929269 |
0.007659695 |
| 92 |
GTF2A1 |
0.0015621043 |
0.0004424363 |
3.5307 |
0.0014554124 |
0.007659695 |
| 78 |
FAM126B |
0.0016794616 |
0.0004804588 |
3.4955 |
0.0015948711 |
0.007659695 |
| 8 |
HPF1 |
0.0014028773 |
0.0004018056 |
3.4914 |
0.0016119759 |
0.007659695 |
| 5 |
YTHDC2 |
0.0007766616 |
0.0002229816 |
3.4831 |
0.0016473638 |
0.007659695 |
| 30 |
SMAP1 |
0.0011067563 |
0.0003182918 |
3.4772 |
0.0016727923 |
0.007659695 |
| 66 |
RFWD2 |
0.0011060594 |
0.0003184453 |
3.4733 |
0.0016896518 |
0.007659695 |
| 7 |
TAB2 |
0.0007931006 |
0.0002298693 |
3.4502 |
0.0017938698 |
0.007659695 |
| 23 |
TMEM87A |
0.0015804243 |
0.0004587707 |
3.4449 |
0.0018187209 |
0.007659695 |
| 44 |
SHFM1 |
0.0015444091 |
0.0004490664 |
3.4392 |
0.0018460187 |
0.007659695 |
| 67 |
SRP9 |
0.0018337032 |
0.0005342287 |
3.4324 |
0.0018784138 |
0.007659695 |
| 13 |
AFF4 |
0.0006706892 |
0.0001960334 |
3.4213 |
0.0019332500 |
0.007659695 |
| 101 |
C16orf91 |
0.0017175196 |
0.0005027810 |
3.4160 |
0.0019597021 |
0.007659695 |
| 50 |
EMC7 |
0.0013912402 |
0.0004078755 |
3.4109 |
0.0019856602 |
0.007659695 |
| 89 |
SUN1 |
0.0017101931 |
0.0005034365 |
3.3970 |
0.0020581868 |
0.007659695 |
| 96 |
NUDT21 |
0.0016457420 |
0.0004861225 |
3.3854 |
0.0021205968 |
0.007659695 |
| 35 |
RPS25 |
0.0015106862 |
0.0004484341 |
3.3688 |
0.0022134174 |
0.007659695 |
| 121 |
FOXJ3 |
0.0013808418 |
0.0004102588 |
3.3658 |
0.0022306790 |
0.007659695 |
| 29 |
RWDD1 |
0.0011509067 |
0.0003435451 |
3.3501 |
0.0023224720 |
0.007659695 |
| 18 |
HNRNPH3 |
0.0012647372 |
0.0003776976 |
3.3485 |
0.0023316964 |
0.007659695 |
| 71 |
PTS |
0.0014024193 |
0.0004198042 |
3.3407 |
0.0023794177 |
0.007659695 |
| 95 |
CUL5 |
0.0007362499 |
0.0002207817 |
3.3347 |
0.0024157500 |
0.007659695 |
| 48 |
VIMP |
0.0008271301 |
0.0002495984 |
3.3138 |
0.0025486009 |
0.007704019 |
| 109 |
X15.Sep |
0.0014147154 |
0.0004289789 |
3.2979 |
0.0026548828 |
0.007704019 |
| 105 |
C8orf59 |
0.0006719449 |
0.0002038512 |
3.2963 |
0.0026658642 |
0.007704019 |
| 27 |
GTF2H1 |
0.0008914960 |
0.0002704685 |
3.2961 |
0.0026667760 |
0.007704019 |
| 11 |
ARFGEF1 |
0.0008873710 |
0.0002727469 |
3.2535 |
0.0029731761 |
0.007845545 |
| 77 |
PTPRN2 |
0.0012859617 |
0.0003954155 |
3.2522 |
0.0029828869 |
0.007845545 |
| 80 |
MFSD14A |
0.0009360301 |
0.0002878697 |
3.2516 |
0.0029874647 |
0.007845545 |
| 49 |
SEC61G |
0.0020590384 |
0.0006333877 |
3.2508 |
0.0029930987 |
0.007845545 |
| 82 |
SLC35B2 |
0.0021351364 |
0.0006575850 |
3.2469 |
0.0030229213 |
0.007845545 |
| 57 |
CCDC90B |
0.0010242649 |
0.0003179770 |
3.2212 |
0.0032271446 |
0.007845545 |
| 3 |
IFNGR1 |
0.0014060444 |
0.0004367476 |
3.2194 |
0.0032422335 |
0.007845545 |
| 45 |
PSMG2 |
0.0011941514 |
0.0003712043 |
3.2170 |
0.0032619120 |
0.007845545 |
| 106 |
FAM91A1 |
0.0010357615 |
0.0003224243 |
3.2124 |
0.0032997260 |
0.007845545 |
| 37 |
PROSER1 |
0.0011413673 |
0.0003557079 |
3.2087 |
0.0033307731 |
0.007845545 |
| 51 |
CYP2J2 |
0.0014743566 |
0.0004618841 |
3.1920 |
0.0034743056 |
0.007845545 |
| 130 |
GTF2H5 |
0.0011014230 |
0.0003452210 |
3.1905 |
0.0034880591 |
0.007845545 |
| 41 |
EBPL |
0.0007688893 |
0.0002420693 |
3.1763 |
0.0036151569 |
0.007845545 |
| 26 |
NDUFC1 |
0.0015680501 |
0.0004967129 |
3.1569 |
0.0037970266 |
0.007845545 |
| 114 |
GTF2F2 |
0.0006693549 |
0.0002121712 |
3.1548 |
0.0038168424 |
0.007845545 |
| 119 |
TXNRD1 |
0.0007296310 |
0.0002314590 |
3.1523 |
0.0038407104 |
0.007845545 |
| 17 |
SLC25A24 |
0.0010227851 |
0.0003250847 |
3.1462 |
0.0039001439 |
0.007845545 |
| 116 |
S100A10 |
0.0010558993 |
0.0003358958 |
3.1435 |
0.0039265077 |
0.007845545 |
| 55 |
SCYL2 |
0.0004753143 |
0.0001513106 |
3.1413 |
0.0039484558 |
0.007845545 |
| 115 |
PPTC7 |
0.0006609633 |
0.0002104917 |
3.1401 |
0.0039606330 |
0.007845545 |
| 64 |
SMAD4 |
0.0009160672 |
0.0002919420 |
3.1378 |
0.0039831227 |
0.007845545 |
| 54 |
CAB39 |
0.0014119311 |
0.0004512431 |
3.1290 |
0.0040727742 |
0.007902398 |
| 32 |
SF3B6 |
0.0013678870 |
0.0004390451 |
3.1156 |
0.0042119097 |
0.007998968 |
| 68 |
CALM2 |
0.0012007113 |
0.0003858570 |
3.1118 |
0.0042521400 |
0.007998968 |
| 73 |
BAG3 |
0.0015235464 |
0.0004904106 |
3.1067 |
0.0043071365 |
0.007998968 |
| 98 |
PDCD6IP |
0.0009606885 |
0.0003098034 |
3.1010 |
0.0043692073 |
0.007999957 |
| 62 |
KIF21A |
0.0008225421 |
0.0002668000 |
3.0830 |
0.0045700555 |
0.008251489 |
| 128 |
KIAA1147 |
0.0005963581 |
0.0001948689 |
3.0603 |
0.0048362312 |
0.008612467 |
| 65 |
CREG1 |
0.0010308321 |
0.0003421173 |
3.0131 |
0.0054381859 |
0.009372111 |
| 123 |
CAPZA2 |
0.0006620910 |
0.0002198170 |
3.0120 |
0.0054528390 |
0.009372111 |
| 19 |
ASCC2 |
0.0005699803 |
0.0001894976 |
3.0078 |
0.0055093102 |
0.009372111 |
| 94 |
CCT2 |
0.0009046769 |
0.0003019182 |
2.9964 |
0.0056672166 |
0.009372111 |
| 84 |
EFCAB14 |
0.0008540047 |
0.0002850813 |
2.9957 |
0.0056781107 |
0.009372111 |
| 91 |
AQP3 |
0.0024864677 |
0.0008311654 |
2.9915 |
0.0057360912 |
0.009372111 |
| 39 |
B4GALT4 |
0.0017972457 |
0.0006012187 |
2.9893 |
0.0057674526 |
0.009372111 |
| 107 |
SIAH2 |
0.0012350764 |
0.0004147259 |
2.9781 |
0.0059303724 |
0.009517882 |
| 22 |
POFUT1 |
0.0008892187 |
0.0003004084 |
2.9600 |
0.0061997147 |
0.009828816 |
| 86 |
JAK1 |
0.0004771416 |
0.0001619528 |
2.9462 |
0.0064146275 |
0.010047007 |
| 97 |
GLOD4 |
0.0005854801 |
0.0002003545 |
2.9222 |
0.0068029642 |
0.010459259 |
| 1 |
RANBP9 |
0.0009830117 |
0.0003367879 |
2.9188 |
0.0068604343 |
0.010459259 |
| 88 |
FBXO8 |
0.0010488456 |
0.0003597726 |
2.9153 |
0.0069192018 |
0.010459259 |
| 9 |
ATG5 |
0.0010437581 |
0.0003614008 |
2.8881 |
0.0073948421 |
0.011049764 |
| 25 |
EIF4H |
0.0007529396 |
0.0002629158 |
2.8638 |
0.0078452615 |
0.011589591 |
| 14 |
TSG101 |
0.0008556847 |
0.0002999327 |
2.8529 |
0.0080554013 |
0.011665544 |
| 100 |
OXSR1 |
0.0006607591 |
0.0002318332 |
2.8501 |
0.0081097911 |
0.011665544 |
| 93 |
MICU2 |
0.0004281525 |
0.0001503710 |
2.8473 |
0.0081658810 |
0.011665544 |
| 87 |
RPL22L1 |
0.0016009073 |
0.0005654542 |
2.8312 |
0.0084910575 |
0.011998233 |
| 112 |
AP3M1 |
0.0008247862 |
0.0002943417 |
2.8021 |
0.0091080859 |
0.012612719 |
| 2 |
DERA |
0.0015372657 |
0.0005487559 |
2.8014 |
0.0091250838 |
0.012612719 |
| 85 |
BSDC1 |
0.0009443511 |
0.0003376053 |
2.7972 |
0.0092169872 |
0.012612719 |
| 10 |
ALDH18A1 |
0.0015523029 |
0.0005566590 |
2.7886 |
0.0094097014 |
0.012619869 |
| 113 |
ZBTB6 |
0.0007549784 |
0.0002707654 |
2.7883 |
0.0094163635 |
0.012619869 |
| 36 |
MYL12B |
0.0013006496 |
0.0004678226 |
2.7802 |
0.0096013205 |
0.012736446 |
| 31 |
EPB41L5 |
0.0006186529 |
0.0002233299 |
2.7701 |
0.0098366966 |
0.012916874 |
| 59 |
GTF2B |
0.0007137483 |
0.0002601489 |
2.7436 |
0.0104813567 |
0.013625764 |
| 24 |
DECR1 |
0.0010005443 |
0.0003670581 |
2.7258 |
0.0109352562 |
0.014075082 |
| 15 |
UBE2A |
0.0011436891 |
0.0004286749 |
2.6680 |
0.0125448260 |
0.015988504 |
| 6 |
THOC3 |
0.0013730551 |
0.0005187582 |
2.6468 |
0.0131862775 |
0.016642874 |
| 58 |
ADAM10 |
0.0007009500 |
0.0002669702 |
2.6256 |
0.0138609473 |
0.017326184 |
| 118 |
GFPT1 |
0.0004352290 |
0.0001681985 |
2.5876 |
0.0151482667 |
0.018754997 |
| 103 |
ZNF654 |
0.0004372436 |
0.0001699650 |
2.5726 |
0.0156880553 |
0.019240068 |
| 56 |
HS6ST1 |
0.0011616253 |
0.0004526650 |
2.5662 |
0.0159215832 |
0.019343980 |
| 46 |
TAF4 |
0.0005904934 |
0.0002309129 |
2.5572 |
0.0162568153 |
0.019568389 |
| 28 |
C2CD5 |
0.0006058432 |
0.0002388042 |
2.5370 |
0.0170360050 |
0.020177406 |
| 43 |
SLC10A3 |
0.0009829393 |
0.0003875876 |
2.5360 |
0.0170731895 |
0.020177406 |
| 81 |
DSCR3 |
0.0007514300 |
0.0002984882 |
2.5175 |
0.0178212235 |
0.020871703 |
| 69 |
OCIAD2 |
0.0011568864 |
0.0004819161 |
2.4006 |
0.0232580559 |
0.026888707 |
| 52 |
RNASEL |
0.0005132963 |
0.0002140144 |
2.3984 |
0.0233724912 |
0.026888707 |
| 76 |
ATP5J |
0.0006059132 |
0.0002764456 |
2.1918 |
0.0368731117 |
0.042048285 |
| 21 |
CCNB1IP1 |
0.0005475081 |
0.0002568260 |
2.1318 |
0.0419336386 |
0.047403244 |
| 34 |
KDM3A |
0.0004990147 |
0.0002381331 |
2.0955 |
0.0452890790 |
0.050755002 |
| 102 |
GPR171 |
-0.0006351095 |
0.0003075104 |
-2.0653 |
0.0482608169 |
0.053623130 |
| 70 |
EBAG9 |
0.0002531786 |
0.0001249288 |
2.0266 |
0.0523249969 |
0.057646183 |
| 90 |
KIAA0196 |
0.0006748153 |
0.0003343753 |
2.0181 |
0.0532499945 |
0.058172263 |
| 74 |
CEBPG |
0.0003382728 |
0.0001691162 |
2.0002 |
0.0552579960 |
0.059862829 |
| 126 |
PPP1CB |
0.0005954306 |
0.0003243724 |
1.8356 |
0.0770533305 |
0.082784570 |
| 110 |
SH2D1A |
-0.0010664737 |
0.0005841488 |
-1.8257 |
0.0785809124 |
0.083733759 |
| 127 |
IFNG.AS1 |
-0.0005213398 |
0.0002889400 |
-1.8043 |
0.0819494161 |
0.086613204 |
| 38 |
ELF1 |
0.0002563900 |
0.0001448954 |
1.7695 |
0.0877048723 |
0.091948656 |
| 42 |
FAM78A |
-0.0004110140 |
0.0003055129 |
-1.3453 |
0.1893153742 |
0.196887989 |
| 122 |
SFMBT2 |
-0.0003342819 |
0.0002749787 |
-1.2157 |
0.2342633810 |
0.241700314 |
| 125 |
HLA.A |
-0.0003110477 |
0.0002589004 |
-1.2014 |
0.2396529390 |
0.245314032 |
| 79 |
FAM161B |
0.0001707463 |
0.0002155638 |
0.7921 |
0.4349670591 |
0.441763419 |
| 12 |
CLEC2D |
-0.0002886735 |
0.0003785102 |
-0.7627 |
0.4520454110 |
0.455549639 |
| 72 |
PARP8 |
-0.0001145582 |
0.0001808481 |
-0.6334 |
0.5315806012 |
0.531580601 |
gene_FunReg(as.matrix(rlog.genesbeta.05.1.raw), isgs.rld.lin[,234], "IFN-beta Genes", "CD4 Counts")
Top Genes from IFN-beta Genes Associated with Outcome: CD4 Counts by p.value (Sample Size = -18801)
| 5 |
C16orf91 |
0.0017175196 |
0.0005027810 |
3.4160 |
0.001959702 |
0.01153491 |
| 3 |
SLC35B2 |
0.0021351364 |
0.0006575850 |
3.2469 |
0.003022921 |
0.01153491 |
| 4 |
AQP3 |
0.0024864677 |
0.0008311654 |
2.9915 |
0.005736091 |
0.01153491 |
| 2 |
B4GALT4 |
0.0017972457 |
0.0006012187 |
2.9893 |
0.005767453 |
0.01153491 |
| 1 |
THOC3 |
0.0013730551 |
0.0005187582 |
2.6468 |
0.013186277 |
0.02109804 |
| 6 |
GPR171 |
-0.0006351095 |
0.0003075104 |
-2.0653 |
0.048260817 |
0.06434776 |
| 7 |
SH2D1A |
-0.0010664737 |
0.0005841488 |
-1.8257 |
0.078580912 |
0.08194942 |
| 8 |
IFNG.AS1 |
-0.0005213398 |
0.0002889400 |
-1.8043 |
0.081949416 |
0.08194942 |
######### scatter plot ######################
######### viral load #####
########## ifn beta
scatter_vl_beta <- function(Symbol){
ggplot(mapping = aes(x = isgs.rld.lin[,235],
y = rlog.genesbeta.05.1.raw[,which(colnames(rlog.genesbeta.05.1.raw) %in% Symbol) ])) +
ylab("rlog transformed counts") +
xlab("Blood HIV Viral Load") +
geom_point(colour = "gray15", size = 2, shape = 20) +
geom_smooth(method = "loess", se = FALSE, colour = "steelblue") +
geom_smooth(method = "lm", se = FALSE, colour = "tomato") +
theme_bw() +
theme(
plot.title = element_text(color="black", size=14, face="bold.italic"),
axis.title.x = element_text(color="black", size=12, face="bold"),
axis.title.y = element_text(color="black", size=12, face="bold"),
axis.text.x = element_text(face="bold", color="black", size=10, angle=0),
axis.text.y = element_text(face="bold", color="black", size=10, angle=0) ) +
annotate("text", x = mean(isgs.rld.lin[,234]),
y = quantile(rlog.genesbeta.05.1.raw[,which(colnames(rlog.genesbeta.05.1.raw) %in% Symbol) ], 0.95),
label = Symbol)
}
for( i in c("THOC3", "AQP3")){
print(scatter_vl_beta(i))
}


################### cd4 counts #####################
############# core ISGs #############
p.irs1 <- ggplot(mapping = aes(x = isgs.rld.lin[,234], y = rlog.isgs.05.raw[,which(colnames(rlog.isgs.05.raw) %in% "IRS1") ])) +
ylab("rlog transformed counts") +
xlab("Blood CD4 counts") +
geom_point(colour = "gray15", size = 2, shape = 20) +
geom_smooth(method = "loess", se = FALSE, colour = "steelblue") +
geom_smooth(method = "lm", se = FALSE, colour = "tomato") +
theme_bw() +
theme(
plot.title = element_text(color="black", size=14, face="bold.italic"),
axis.title.x = element_text(color="black", size=12, face="bold"),
axis.title.y = element_text(color="black", size=12, face="bold"),
axis.text.x = element_text(face="bold", color="black", size=10, angle=0),
axis.text.y = element_text(face="bold", color="black", size=10, angle=0) ) +
annotate("text", x = mean(isgs.rld.lin[,234]),
y = quantile(rlog.isgs.05.raw[,which(colnames(rlog.isgs.05.raw) %in% "IRS1") ], 0.95),
label = "IRS1")
p.irs1

scatter_cd4counts_isgs <- function(Symbol){
ggplot(mapping = aes(x = isgs.rld.lin[,234], y = rlog.isgs.05.raw[,which(colnames(rlog.isgs.05.raw) %in% Symbol) ])) +
ylab("rlog transformed counts") +
xlab("Blood CD4 counts") +
geom_point(colour = "gray15", size = 2, shape = 20) +
geom_smooth(method = "loess", se = FALSE, colour = "steelblue") +
geom_smooth(method = "lm", se = FALSE, colour = "tomato") +
theme_bw() +
theme(
plot.title = element_text(color="black", size=14, face="bold.italic"),
axis.title.x = element_text(color="black", size=12, face="bold"),
axis.title.y = element_text(color="black", size=12, face="bold"),
axis.text.x = element_text(face="bold", color="black", size=10, angle=0),
axis.text.y = element_text(face="bold", color="black", size=10, angle=0) ) +
annotate("text", x = mean(isgs.rld.lin[,234]),
y = quantile(rlog.isgs.05.raw[,which(colnames(rlog.isgs.05.raw) %in% Symbol) ], 0.95),
label = Symbol)
}
## plot
for(i in c("IRS1", "MVB12A", "ODF3B","LGALS3BP", "UBA7", "MYD88","LAG3","TRIM69", "PSMB9", "PSME2")){
print(scatter_cd4counts_isgs(Symbol = i))
}










## PCA with important genes with TMM NORMARLIZED data
########## pcd by filtered core ISGs 0.05 log2 FC 1
## PCA of prcomp
# pc <- princomp(cnts_f, cor=TRUE, scores=TRUE)
# pc$scores
cnts.edger.isg.05.1 <- t(cnts.edger[rownames(cnts.edger) %in% isgs.edger.05.1$Gene_ID, ])
sum(colnames(cnts.edger.isg.05.1 ) != isgs.edger.05.1$Gene_ID)
## [1] 0
colnames(cnts.edger.isg.05.1 ) <- isgs.edger.05.1$Symbol.x
edger.pca.isgs.05.1 <- prcomp(cnts.edger.isg.05.1 ,
center = TRUE, scale. = TRUE, retx = TRUE)
plot(edger.pca.isgs.05.1)

pca3d(edger.pca.isgs.05.1, components = 1:3, col= c(rep("steelblue", 13), rep("tomato", 19)),
title = "Core ISGs with FDR 0.05 and log2 FC 1",
radius = 1.5, show.labels = TRUE)
## [1] 0.8605787 0.1640156 0.1363777
## 'princomp' can only be used with more units than variables
## pc <- princomp(t(cnts.edger[rownames(cnts.edger) %in% isgs.edger.05.1$Gene_ID, ]), cor=TRUE, scores=TRUE)
getwd()
## [1] "/home/guanshim/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataRaw"
######## key genes
###### LAG3 ODF3B
num.keygenes <- which( rownames(edger.pca.isgs.05.1$rotation) %in% c("LAG3", "ODF3B","NLRC5") )
plot3d(edger.pca.isgs.05.1$x[,1:3], col= c(rep("steelblue", 13), rep("tomato", 19)) ,
size = 1, type = 's')
text3d(edger.pca.isgs.05.1$rotation[num.keygenes,1:3]*20,
texts=rownames(edger.pca.isgs.05.1$rotation)[num.keygenes], col="black", justify = "left",
font = 5)
coords <- NULL
for (i in num.keygenes) {
coords <- rbind(coords, rbind(c(0,0,0),edger.pca.isgs.05.1$rotation[i,1:3]*20))
}
lines3d(coords, col="black", lwd=2)
# # add legend
# legend3d("topright", legend = paste( c('Health Control',
# 'HIV Infected')),
# pch = 16, col = c("steelblue", "tomato"), cex=1, inset=c(0.02))
#
# # capture snapshot
# # snapshot3d(filename = '3dplot.png', fmt = 'png')
#
# ######### snapshot
# rgl.bringtotop()
# rgl.viewpoint(0, 20)
# rgl.snapshot("test.png")
## # all integer in cnts_f, filtered counts
### cnts cnts.edger cnts.deseq2 cnts.tpm
## var.cnts.rld rlog transformed counts, based on DESeq2 normalization
## pca
## edger.pca.isgs.05.1$x the matrix define the scatter of points, 1 to 13 health control
## explore scater
# the counts data
# data("sc_example_counts")
#
# ## the dataframe has condition information
# data("sc_example_cell_info")
#
# example_sce <- SingleCellExperiment(
# assays = list(counts = sc_example_counts),
# colData = sc_example_cell_info)
rna_info <- data.frame(pid = rna.pid, Group = as.factor(c(rep("Control", 13),
rep("HIV Infected", 19)
)) )
rna_info$Group %<>% relevel("Control")
## cnts. list
cnts.list <- list(cnts_f, cnts.edger, cnts.deseq2, cnts.tpm)
cnts.names <- c("Filtered Counts", "TMM Normalized Counts",
"DESeq2 Normalized Counts", "TPM Normalized Counts")
for (i in 1:4){
j = cnts.list[[i]]
## using scater, start with an object
example_sce <- SingleCellExperiment(
assays = list(counts = j),
colData = rna_info)
## RLE plots
print( scater::plotRLE(example_sce, exprs_values = "counts", exprs_logged = FALSE,
colour_by = "Group", style = "minimal") + scale_x_discrete("Samples", labels = rna.pid) + labs(caption = paste("RLE Plot:" ,cnts.names[i]) ) )
## pca plots
example_sce <- SingleCellExperiment(
assays = list(logcounts = j),
colData = rna_info)
print( scater::plotPCA(example_sce, colour_by = "Group", size_by = "Group") + labs(caption = paste( "PCA Plot:",cnts.names[i]) ))
}








## define the gene list
invitro_genes <- c("Mx2", "APOBEC3G", "Siglec1", "ISG15", "Bst2")
## turn in to upper case
invitro_genes[ sapply(invitro_genes, toupper) %nin% res.edger.05$Symbol ]
## character(0)
invitro_genes[ sapply(invitro_genes, toupper) %nin% res.edger.05.1$Symbol ]
## character(0)
## check
# "CD169" %in% res.edger.05$Symbol
# "TETHERIN" %in% res.edger.05$Symbol
# "CD169" %in% res.edger.order$Symbol
# "TETHERIN" %in% res.edger.order$Symbol
"CD169" %in% cnts.raw$Symbol
## [1] FALSE
"TETHERIN" %in% cnts.raw$Symbol
## [1] FALSE
# "CD169" %in% isgs$Symbol
# "TETHERIN" %in% isgs$Symbol
# "CD169" %in% genesbeta$Symbol
# "TETHERIN" %in% genesbeta$Symbol
##
cnts.raw[ cnts.raw$Symbol %in% "APOBEC3G", ]
## Gene_ID Symbol Length C138 C178 C255 C278 C361 C404 C493
## 28642 ENSG00000239713.7 APOBEC3G 5454 7 14 28 34 55 121 23
## C582 C708 C716 C914 C947 C972 H124 H132 H154 H188 H217 H286 H307
## 28642 43 30 250 58 31 91 26 69 60 175 38 29 55
## H323 H391 H428 H594 H622 H648 H683 H819 H825 H839 H965 H998
## 28642 145 58 57 351 52 38 14 54 29 71 10 874
## a fold change is the ratio of the averages
vitro_table_seq <- res.edger.05[res.edger.05$Symbol %in% sapply(invitro_genes, toupper),c(4,1,5)]
vitro_table_seq[4,] <- c("Tetherin", "", "")
vitro_table_seq[5,] <- c("CD169", "", "")
colnames(vitro_table_seq) <- c("Symbol", "RNA-Seq logFC","FDR")
vitro_table_seq
## Symbol RNA-Seq logFC FDR
## ENSG00000088827.12 SIGLEC1 1.44607274125171 2.26773427023047e-05
## ENSG00000187608.8 ISG15 2.54287395182648 2.59693492042342e-05
## ENSG00000239713.7 APOBEC3G 1.13486956678948 0.000115248584431884
## ENSG00000130303.12 Tetherin
## ENSG00000183486.12 CD169
############## RECHECK vitro genes#########################
## read in all clinical data
clinical_ready <- read_excel("~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/clinical_ready.xlsx")
## clinical_ready <- unlist(clinical_ready)
clinical_ready <- as.data.frame(clinical_ready)
# factor(clinical_ready$Group)
# clinical_ready$Group %<>% relevel("control")
for(j in 1:5){
i = c(22,20,19,21,23)[j]
t_vitro = t.test(clinical_ready[,i] ~ clinical_ready$Group)
vitro_table_seq[j,4] <-round(log2(t_vitro$estimate[2] - t_vitro$estimate[1]),2)
vitro_table_seq[j,5] <- round(t_vitro$p.value,5)
colnames(vitro_table_seq)[c(4,5)] <- c("qRT-PCR logFC", "t-test p.value")
}
kable(vitro_table_seq, digits = c(2,2,2,2,5))
| ENSG00000088827.12 |
SIGLEC1 |
1.44607274125171 |
2.26773427023047e-05 |
3.79 |
0.18595 |
| ENSG00000187608.8 |
ISG15 |
2.54287395182648 |
2.59693492042342e-05 |
5.61 |
0.00168 |
| ENSG00000239713.7 |
APOBEC3G |
1.13486956678948 |
0.000115248584431884 |
7.01 |
0.15129 |
| ENSG00000130303.12 |
Tetherin |
|
|
7.73 |
0.00478 |
| ENSG00000183486.12 |
CD169 |
|
|
2.27 |
0.28773 |
# formatC(numb, format = "e", digits = 2)
## format(res.edger[which.min(res.edger$PValue), ]$FDR,digits=2,scientific=TRUE )
## formatC
## prettyNum()
############## get dataet ready for association test ###########
dim(clinical_ready)
## [1] 38 24
clinical_ready$pid[1:24] <- gsub("MIHIV", "H", clinical_ready$pid[1:24])
clinical_ready$pid[25:38] <- gsub("MIHIV", "C", clinical_ready$pid[25:38])
clinical <- clinical_ready[clinical_ready$pid %in% rna.pid, ]
dim(clinical)
## [1] 32 24
## now we have data clinical
## using FDR 0.05 cutoff to get the rlog data ready
## isgs.edger.05 has the gene symbol list
length(unique(isgs$Symbol)) == nrow(isgs) ## every symbol in isgs is unique
## [1] TRUE
length(unique(genesbeta$Symbol)) == nrow(genesbeta)
## [1] TRUE
nrow(isgs); nrow(genesbeta)
## [1] 230
## [1] 423
length(unique(res.edger$Symbol)) == nrow(res.edger)
## [1] FALSE
## res.edger
sum(res.edger$Symbol != cnts_fsym$Symbol )
## [1] 0
paste("Using Symbol as identifier")
## [1] "Using Symbol as identifier"
######### isgs #############
isgs.edger <- res.edger[ res.edger$Symbol %in% isgs$Symbol, ]
nrow(isgs.edger) == nrow(isgs)
## [1] TRUE
## 117 genes out of 230 FDR 0.05 in ISGs.
nrow(isgs.edger[ isgs.edger$FDR <= 0.05, ] )
## [1] 117
## ranked by logFC
isgs.save <- isgs.edger[base::order(isgs.edger$logFC, decreasing = TRUE), c(4,1,5)]
isgs.save$Gene_ID <- row.names(isgs.save)
write.xlsx(isgs.save,
"~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/ISGs_DEanalysis_results.xlsx",
sheetName="ISGs Results")
######## genes beta ##############
genesbeta.edger <- res.edger[ res.edger$Symbol %in% genesbeta$Symbol, ]
genesbeta$Symbol [genesbeta$Symbol %nin%res.edger$Symbol]
## [1] "SEPT15"
genesbeta.edger[423,] <- res.edger[row.names(res.edger) == genesbeta$Gene_ID [genesbeta$Symbol %nin%res.edger$Symbol] , ]
nrow(genesbeta.edger) == nrow(genesbeta)
## [1] TRUE
# 130 genes out of 423 FDR IFN-beta genes.
genesbeta.edger[423,4] <- genesbeta$Symbol [genesbeta$Symbol %nin%res.edger$Symbol]
nrow(isgs.edger[ genesbeta.edger$FDR <= 0.05, ] )
## [1] 130
genesbeta.save <- genesbeta.edger[base::order(genesbeta.edger$logFC, decreasing = TRUE), c(4,1,5)]
genesbeta.save$Gene_ID <- row.names(genesbeta.save)
write.xlsx(genesbeta.save,
"~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/IFNbeta_DEanalysis_results.xlsx",
sheetName="IFNbeta Results")
### by the way, save data file
## rlog transformed data
sum(var.rld$Gene_ID != row.names(cnts_fsym))
## [1] 0
var.rld.save <- var.rld %>% dplyr::mutate(Symbol = cnts_fsym$Symbol) %>% dplyr::select(Gene_ID, Symbol, everything())
write.xlsx(var.rld.save,
"~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/rlog_counts_linear_regression.xlsx",
sheetName="rlog transformed counts")
## TMM normalized counts
sum(row.names(cnts.edger) != row.names(cnts_fsym))
## [1] 0
cnts.edger <- data.frame(cnts.edger) %>% dplyr::mutate(Symbol = cnts_fsym$Symbol,
Gene_ID = row.names(cnts_fsym)) %>% dplyr::select(Gene_ID, Symbol, everything())
write.xlsx(cnts.edger,
"~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/TMM_normalized_counts.xlsx",
sheetName="TMM Normalized Counts")
## ## gene level dataset
var.isgs.05 <- base::merge(var.rld, isgs.edger.05, by = "Gene_ID") %>% dplyr::mutate(Symbol = Symbol.x) %>%
select(-c(Symbol.x, Symbol.y))
dim(var.isgs.05)
## [1] 117 39
isgs.05.lin <- t(var.isgs.05[2:33])
base::colnames(isgs.05.lin) <- var.isgs.05$Symbol
head(isgs.05.lin)
## LAP3 CD38 ETV7 SLC38A5 TYMP SP100 IFI35
## C138 9.867168 7.336852 5.265898 5.344793 7.451812 9.791733 7.090217
## C178 9.950874 6.977888 5.612663 6.077553 7.600146 10.135759 7.897387
## C255 9.118263 7.748172 5.186480 5.764030 7.670709 9.731154 7.253083
## C278 9.213961 7.159973 5.296277 5.826512 7.572017 9.992123 7.300156
## C361 9.663467 7.103657 4.736297 6.215137 7.165661 9.704992 7.288406
## C404 9.136345 7.886301 4.809632 5.730389 7.956326 9.964701 7.171943
## SP140 CHMP5 LAG3 APOL1 PSME2 REC8 SAMHD1
## C138 7.709532 10.94266 4.986371 9.460319 10.37938 5.388783 9.999569
## C178 7.432788 11.21895 5.613652 9.790280 11.08450 5.889420 10.554656
## C255 8.104026 11.06322 5.294884 9.368548 11.03126 5.867115 10.304422
## C278 6.952975 11.76710 5.159817 9.131094 11.04412 5.896007 9.836114
## C361 7.311101 11.61045 5.323891 8.964239 10.91123 5.921864 9.867448
## C404 8.190129 11.30712 5.420391 9.322799 10.65937 6.034906 10.274697
## MYL12A TNFSF13B PARP4 PRKD2 C1GALT1 LGALS3BP DHX58
## C138 11.17281 8.130499 9.066054 8.252985 9.014917 10.77799 5.727563
## C178 11.38042 8.066374 9.153046 8.503493 8.724409 11.07755 5.728420
## C255 10.65238 7.748719 8.588581 8.811400 8.997730 10.73626 5.215642
## C278 11.57600 7.511480 8.527750 8.339072 8.891866 10.59244 5.983675
## C361 11.64601 7.640374 8.873504 8.103907 9.000729 10.52817 5.893568
## C404 10.98787 8.119275 8.848614 8.702689 8.775256 10.21630 5.768037
## UNC93B1 OAS3 OAS2 TRIM38 CCND3 STAT1 IL18R1
## C138 7.965627 7.726339 6.718739 9.852707 9.565314 10.84371 4.601134
## C178 8.237653 8.983912 7.672037 9.803508 10.219838 11.11737 4.723471
## C255 8.289397 7.651487 6.611298 9.874578 10.158971 10.56483 4.620602
## C278 8.299603 7.348360 6.274571 9.608837 9.925488 10.73226 4.323713
## C361 8.410317 8.427393 7.260259 9.611912 9.786995 10.89416 4.444497
## C404 8.206400 7.745942 7.106949 10.153835 9.725215 10.39885 4.522014
## FBXO6 GBP1 IFIT3 IFIT2 CD274 KIAA1217 TNFSF10
## C138 5.003868 9.139211 7.501533 6.015248 5.338770 10.355345 11.09513
## C178 3.787595 9.248674 8.963836 6.625020 5.322851 10.347544 11.38707
## C255 4.005208 8.857872 7.815193 5.832549 4.660256 10.111145 11.12764
## C278 4.236622 8.591121 7.499523 6.344849 4.500908 9.955803 10.96267
## C361 4.477857 8.930270 8.249221 6.748019 5.034493 9.863574 11.13880
## C404 4.161270 8.874294 7.519459 6.203888 4.981542 9.933349 11.08739
## NMI ZNFX1 ZBP1 RBCK1 IFI6 HELB APOL2
## C138 8.879147 10.94410 5.534583 9.963079 7.432346 6.846203 7.930116
## C178 9.153233 11.62872 5.544376 10.287090 9.315082 6.543527 7.920226
## C255 9.182702 11.48319 5.780766 10.115637 8.095368 6.609950 7.838573
## C278 9.187906 10.99790 5.706764 9.831691 7.628337 6.173100 7.682485
## C361 9.188313 10.92552 5.627104 10.426229 8.911853 6.423068 7.329808
## C404 9.115414 10.96949 6.078898 10.256537 7.857635 6.843940 7.786696
## BST2 C19orf66 TRIM22 XAF1 ALOX5AP CMPK2 OASL
## C138 8.726533 6.333910 6.774194 3.566828 7.460396 6.191025 5.021954
## C178 9.555783 7.046591 6.611383 4.015281 7.342391 7.589287 6.155258
## C255 8.605017 6.485834 5.813885 3.141123 7.695262 6.559806 4.832530
## C278 7.984982 6.645712 6.303658 3.020560 7.196080 6.047281 4.917173
## C361 8.473594 6.358566 6.539023 3.314071 7.258339 7.161630 5.317548
## C404 8.663469 6.722197 6.692724 3.269448 7.331682 5.986126 4.808287
## SP110 CHST12 TANK STX17 DDX60 IFI44L IFI44
## C138 6.947574 8.078528 8.387527 9.203141 9.173186 6.881194 5.594663
## C178 7.596500 8.056324 7.934763 9.069404 9.456895 8.569643 6.205046
## C255 7.564098 8.276962 7.977235 8.865010 9.359979 6.416108 5.479508
## C278 6.949771 8.121394 7.991880 8.740922 8.936877 6.158686 5.243370
## C361 7.165068 8.032650 7.990631 8.692286 9.184433 7.718653 5.978889
## C404 7.824620 8.371947 8.072107 8.880781 9.125415 7.095347 6.028525
## HERC6 SCARB2 PML NLRC5 MVB12A IFITM3 STOM
## C138 7.082148 10.95466 8.445142 9.516829 8.254245 9.881029 7.523498
## C178 7.022916 11.05517 8.451560 9.783022 8.568110 10.718180 8.047615
## C255 6.438577 10.91390 8.513692 9.515867 8.386849 9.979657 8.070004
## C278 6.114776 11.00890 8.141005 9.432672 8.557906 10.126281 7.867171
## C361 6.499733 10.95588 8.401874 9.351876 8.647557 10.328901 8.333952
## C404 6.454427 10.84901 8.703075 9.632505 8.374965 10.268266 8.227322
## GBP5 MOV10 UBE2L6 MX1 ADAR LY6E DBF4B
## C138 6.336614 8.466466 7.272812 7.813249 10.52543 7.085606 4.842481
## C178 5.705942 9.044902 8.026372 9.585274 10.76889 8.456576 3.983493
## C255 5.919303 8.845355 7.533258 8.329676 10.54218 7.475427 4.063600
## C278 5.451388 9.165195 7.653039 7.926153 10.39614 6.678364 4.860282
## C361 5.816386 8.806109 7.608277 9.078435 10.70760 7.546236 4.294282
## C404 6.123406 8.737321 7.732068 8.256320 10.49360 7.612038 4.416107
## GBP4 GPR155 AZI2 AIM2 DTX3L IFI27 SLFN5
## C138 8.529817 8.086467 6.814825 6.231773 11.29703 11.51818 8.966061
## C178 7.858861 8.578279 7.132662 5.435133 11.45445 13.04815 9.102441
## C255 7.682635 8.242406 6.892564 6.318103 11.11370 11.92002 9.107625
## C278 7.349399 7.951212 7.094988 5.033731 10.85467 12.01468 8.597985
## C361 7.491534 7.733353 7.100754 5.182821 11.17303 12.15507 8.789994
## C404 8.308006 8.536933 6.908094 6.578155 10.92740 12.02965 9.457419
## TTC21A LGALS9 IRS1 TRIM56 STAT2 GIMAP8 AFF1
## C138 4.968966 10.81991 8.468684 11.66373 8.819694 7.311638 9.995448
## C178 4.763164 11.45751 8.390885 11.43215 9.298423 7.397807 9.403079
## C255 4.920011 10.78248 8.226115 11.48749 8.731979 7.520484 9.149224
## C278 5.325477 10.81892 8.274534 11.04144 8.733535 7.069483 9.484531
## C361 5.004796 10.86634 8.439736 11.03074 8.999026 7.316083 9.550837
## C404 5.641098 10.60490 8.074706 11.42530 8.876508 7.762367 9.315399
## MYD88 PARP14 CNP RNF213 SAMD9L ODF3B PARP10
## C138 7.775971 10.75676 9.180904 11.61643 8.108618 4.523807 6.007590
## C178 7.732984 11.26269 9.886882 11.63361 8.347977 5.394195 5.302252
## C255 7.516481 10.87403 9.989909 11.22789 7.809400 4.576150 4.703562
## C278 7.816578 10.41137 10.015216 11.04443 7.731642 4.447842 4.450865
## C361 8.066496 10.61647 9.975362 11.10154 7.805622 4.659145 4.897326
## C404 7.652995 10.71523 9.980377 11.45343 8.122967 4.751042 4.472218
## UBA7 MX2 USP18 IFITM2 ANKFY1 IFIT1 TRIM69
## C138 8.244770 6.749004 6.136317 8.553788 7.891190 5.999668 7.589825
## C178 9.223529 7.810126 6.333246 9.059867 8.026412 7.445089 8.388108
## C255 8.635938 6.850528 5.442809 8.575567 7.972685 6.187003 8.378468
## C278 9.024796 6.065249 5.186643 8.697561 7.775830 6.065008 8.054269
## C361 8.654065 7.311785 5.906347 8.906111 7.714518 7.035476 8.219317
## C404 8.805285 7.063777 5.254531 8.784621 7.917644 6.067769 7.923164
## ISG15 FANCA TDRD7 SPATS2L CASP4 C5orf56 TMEM229B
## C138 8.377585 6.469951 8.221025 11.59267 7.689389 8.868314 6.873944
## C178 9.825577 6.196865 7.958057 11.93156 7.796336 8.908331 7.138878
## C255 8.852359 5.926922 7.242217 11.73400 8.013439 9.221513 7.009965
## C278 8.321250 6.211021 8.579315 11.56528 8.311130 9.057595 6.432438
## C361 9.479884 6.015680 8.976217 11.67828 8.106555 8.946800 6.424325
## C404 8.048303 6.391277 8.268819 11.41536 8.197493 9.437667 7.226240
## RNY4P34 ASAH2B SAMD9 IRF9 APOL6 GBP1P1 AC009950.2
## C138 4.203755 6.599064 9.934268 5.921198 10.73782 7.262405 4.204009
## C178 4.633452 5.418369 10.171459 6.206743 10.85580 7.341981 4.120620
## C255 4.558134 5.570287 9.819433 5.763945 10.48934 6.940027 3.986011
## C278 3.778029 6.237194 9.165397 5.692933 10.35632 6.758027 3.484288
## C361 4.243922 6.458028 9.707812 5.967228 10.37614 7.063865 3.019480
## C404 4.367714 6.066408 9.283845 6.102632 10.47377 7.002595 3.855110
## TRIM26 APOBEC3G PSMB9 RP11-468E2.4 RP3-508I15.21
## C138 7.879629 5.188599 9.570190 4.689973 6.826668
## C178 8.507592 5.417215 9.953556 5.287758 6.762121
## C255 8.074444 5.001081 9.902093 4.710582 7.317144
## C278 8.008540 5.078251 9.744306 4.616824 6.538506
## C361 8.284961 5.399453 9.459633 4.672685 6.384693
## C404 7.945313 5.681959 9.842796 4.789148 6.523451
write.csv(isgs.05.lin,
"~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/corr/isgs.05.lin.csv",
row.names = T)
var.genesbeta.05 <- base::merge(var.rld, genesbeta.edger.05, by = "Gene_ID") %>% dplyr::mutate(Symbol = Symbol.x) %>% select(-c(Symbol.x, Symbol.y))
dim(var.genesbeta.05)
## [1] 130 39
genesbeta.05.lin <- t(var.genesbeta.05[2:33])
base::colnames(genesbeta.05.lin) <- var.genesbeta.05$Symbol
head(genesbeta.05.lin)
## RANBP9 DERA IFNGR1 GRN YTHDC2 THOC3 TAB2
## C138 7.912959 8.467951 8.032676 11.37987 9.085536 5.289209 8.875657
## C178 7.313436 8.040656 7.476750 11.59055 8.392548 4.447393 8.542364
## C255 7.240274 7.895358 7.289176 11.53423 8.345247 4.269049 8.108490
## C278 7.565216 8.642894 7.506008 11.47378 8.709332 5.612749 8.437504
## C361 7.643647 8.501790 8.366683 11.50874 8.716034 6.272993 8.598325
## C404 7.218674 8.038162 7.309357 11.33581 8.556872 5.206325 8.498012
## HPF1 ATG5 ALDH18A1 ARFGEF1 CLEC2D AFF4 TSG101
## C138 8.046934 7.308089 10.055805 10.31783 6.846755 10.24822 9.182325
## C178 8.033683 6.897603 9.460179 10.26381 6.464322 10.31153 9.024248
## C255 8.069564 6.834655 9.239293 10.16028 7.454161 10.33347 8.838860
## C278 8.420149 7.489185 9.680300 10.26754 6.811138 10.22962 9.212177
## C361 8.733115 7.516829 10.009360 10.28749 6.654229 10.13261 9.310590
## C404 8.355548 6.922905 9.384865 10.20863 8.234129 10.27133 8.876081
## UBE2A AK6 SLC25A24 HNRNPH3 ASCC2 TIMM9 CCNB1IP1
## C138 9.301149 6.486911 10.630100 10.92436 7.930829 5.912848 7.019444
## C178 9.146197 5.665633 10.097595 10.70382 8.033779 6.461367 7.645393
## C255 9.019654 5.744862 9.976250 10.22431 7.788379 6.347257 7.658999
## C278 9.582983 6.573267 10.370583 11.09048 7.863068 6.670263 7.921531
## C361 9.485932 6.473735 10.301553 11.12113 8.046687 6.704238 7.566868
## C404 8.992791 6.113313 9.984596 10.67578 7.826735 6.418004 7.471797
## POFUT1 TMEM87A DECR1 EIF4H NDUFC1 GTF2H1 C2CD5
## C138 8.379680 10.533445 10.17962 9.863095 9.593266 8.503443 7.601580
## C178 8.431403 9.965530 10.73064 9.990593 9.527227 7.918540 7.446185
## C255 7.998853 9.672223 10.42071 9.591888 9.152657 8.054602 6.621312
## C278 8.519501 10.706782 10.92109 10.105240 10.181007 8.444837 7.276353
## C361 8.563552 10.714028 10.78561 10.056841 10.083055 8.611393 7.203087
## C404 8.377200 10.264654 10.48951 9.676580 9.628575 8.278868 7.493229
## RWDD1 SMAP1 EPB41L5 SF3B6 UNC50 KDM3A RPS25
## C138 10.35054 8.797346 7.375660 9.065811 7.165796 9.588798 11.23493
## C178 10.46211 8.925759 7.151401 8.898266 7.012972 8.739400 11.31899
## C255 10.21933 9.023045 7.040121 8.644359 6.602051 9.082361 10.58428
## C278 10.80311 9.238505 7.219020 9.387477 7.406792 9.273106 11.91670
## C361 10.82343 9.033970 7.206370 9.468090 7.830609 9.184926 11.69869
## C404 10.33352 9.064126 7.276992 8.756893 7.022273 9.325140 11.54058
## MYL12B PROSER1 ELF1 B4GALT4 KHDRBS1 EBPL FAM78A
## C138 12.64165 8.506940 9.866024 9.259312 11.30856 7.543688 4.934094
## C178 11.65453 7.997582 9.592103 9.496596 11.10801 7.373432 5.344063
## C255 11.02457 8.051141 9.503906 9.361085 10.89436 7.679217 5.110267
## C278 12.28996 8.251018 9.503641 9.877419 11.06087 8.034764 4.643207
## C361 12.47040 8.302336 9.374101 9.787754 11.27414 8.165088 4.470133
## C404 11.46661 8.342810 9.377081 9.547380 10.80602 7.808805 5.390242
## SLC10A3 SHFM1 PSMG2 TAF4 ZNF227 VIMP SEC61G
## C138 6.325477 11.23752 7.912083 7.161471 7.545659 12.09743 11.08039
## C178 7.021074 11.35196 7.721595 6.786061 7.084397 12.23990 10.46148
## C255 6.581205 11.23758 7.387654 6.522174 6.506294 12.07738 10.05071
## C278 6.747413 11.92575 8.040301 6.888923 6.867026 12.38673 10.95365
## C361 7.027952 11.69249 8.283434 6.915254 7.237013 12.37564 11.12747
## C404 6.393719 11.35031 7.655660 6.642907 6.961358 11.87129 10.31730
## EMC7 CYP2J2 RNASEL DHX9 CAB39 SCYL2 HS6ST1
## C138 8.610379 8.588126 8.039482 10.62800 10.056704 9.934338 7.245874
## C178 8.991694 8.099976 8.038297 10.34589 9.425507 9.827171 6.978170
## C255 8.850531 7.788425 7.836313 10.14056 8.974988 9.949297 6.668056
## C278 9.325157 8.678366 7.876922 10.28880 9.290417 10.052397 6.908562
## C361 9.427992 8.606511 8.171808 10.72600 9.609573 9.964744 7.200230
## C404 8.977129 8.288689 8.053697 10.18027 8.909856 9.721596 6.633800
## CCDC90B ADAM10 GTF2B NUP54 USO1 KIF21A DCAF5
## C138 8.027229 9.959413 7.627672 6.445870 9.555883 10.449762 10.21670
## C178 8.469407 9.670550 7.184545 6.690508 9.285799 10.241753 10.15591
## C255 8.069241 9.586612 7.203819 6.450134 9.173302 10.096999 10.00452
## C278 8.797365 9.760111 7.920632 6.684319 9.293357 10.135767 10.47012
## C361 8.728659 9.702383 7.617342 6.842722 9.491616 10.271184 10.32877
## C404 8.642170 9.583363 7.502119 6.609856 9.212789 9.923844 10.25746
## SMAD4 CREG1 RFWD2 SRP9 CALM2 OCIAD2 EBAG9
## C138 9.610483 7.846309 9.061319 8.484599 12.97527 9.847118 9.243576
## C178 9.430839 7.258670 8.691441 8.420350 13.10802 10.243971 8.894444
## C255 9.311670 6.949061 8.560335 7.855760 12.73698 9.975542 8.953605
## C278 9.608276 7.871398 8.768623 8.740858 13.52161 10.614304 9.426707
## C361 9.661061 7.895946 8.985741 8.881866 13.52336 10.307957 9.246684
## C404 9.622513 7.428793 8.740053 8.351744 13.04120 10.006420 9.033590
## PTS PARP8 BAG3 CEBPG TCEB1 ATP5J PTPRN2
## C138 6.910454 7.080617 8.671210 9.914757 8.692755 10.77544 7.085429
## C178 6.728874 6.927890 8.790847 9.706797 8.089237 11.02052 6.841898
## C255 6.704771 7.181084 8.115995 9.457525 8.097156 10.84772 7.225210
## C278 7.681382 7.388577 8.995560 9.525587 8.680314 11.63203 7.326048
## C361 7.755580 7.154215 9.417610 9.656750 8.766745 11.61914 7.697379
## C404 7.171029 7.476350 8.361631 9.008379 8.167808 10.77545 7.066696
## FAM126B FAM161B MFSD14A DSCR3 SLC35B2 UBR1 EFCAB14
## C138 9.160295 5.686094 7.925271 7.348987 7.078676 8.818645 10.62260
## C178 9.525485 5.658328 7.299293 7.159782 6.055272 8.550152 10.31966
## C255 9.012089 5.466551 7.104083 6.984556 5.079008 8.085313 10.40801
## C278 9.368694 6.050068 7.555551 7.458667 6.909885 8.367418 10.53853
## C361 8.873797 5.358568 7.523089 7.505641 7.170605 8.452426 10.41380
## C404 9.142402 5.706008 7.347915 7.160959 5.886688 8.421015 10.12901
## BSDC1 JAK1 RPL22L1 FBXO8 SUN1 KIAA0196 AQP3
## C138 9.209910 10.82342 8.277954 6.317907 9.523450 7.483559 7.610544
## C178 8.470785 10.63546 8.711431 6.010072 9.360754 7.116432 5.885082
## C255 7.983212 10.59104 9.228488 5.825525 9.068991 6.751885 5.691626
## C278 8.919265 10.54603 9.441436 6.514749 10.090808 7.348790 6.197738
## C361 8.948486 10.62324 9.425701 6.698234 9.912969 7.327842 8.070644
## C404 8.675502 10.56443 8.886327 6.492482 9.769901 6.844814 6.607986
## GTF2A1 MICU2 CCT2 CUL5 NUDT21 GLOD4 PDCD6IP
## C138 9.824951 8.439502 10.06750 9.300668 9.636233 9.966755 11.07782
## C178 9.434693 8.373941 10.44579 9.047694 8.637358 9.915884 10.78393
## C255 9.338843 8.200687 10.37385 9.154837 8.519740 9.664733 10.28274
## C278 9.796509 8.580147 10.52313 9.333916 9.411391 10.141589 10.75321
## C361 10.134565 8.727558 10.91102 9.342102 9.688949 10.050345 10.88336
## C404 9.801327 8.291544 10.07014 9.227766 8.967173 9.738636 10.45182
## MUS81 OXSR1 C16orf91 GPR171 ZNF654 EIF1AD C8orf59
## C138 7.850039 10.245778 6.595786 4.889941 8.054778 7.230849 6.445047
## C178 7.933027 10.238566 6.899864 5.198771 8.022355 6.720894 6.656162
## C255 7.638330 10.021866 6.543896 5.025987 8.007562 6.526501 6.593823
## C278 8.627114 10.110092 7.522810 5.025601 8.079514 7.306451 6.816486
## C361 8.554114 10.280295 7.782282 5.140745 8.098356 7.884656 6.798592
## C404 8.209877 9.850426 7.060260 5.218572 7.919348 7.148286 6.824996
## FAM91A1 SIAH2 FAM89A 15-Sep SH2D1A CSF1 AP3M1
## C138 9.489363 8.539215 5.617279 9.083014 4.811108 7.151049 7.500924
## C178 9.153787 8.395778 5.655119 8.841426 4.642196 6.410664 7.658200
## C255 9.104821 8.656440 5.777134 9.330500 5.155980 6.211862 7.249858
## C278 9.208268 9.121091 5.976334 9.063734 4.731150 6.560373 7.707178
## C361 9.346002 9.024605 5.941615 9.382634 5.098159 6.984101 7.712960
## C404 9.061254 8.857020 5.607681 9.269751 5.857660 6.929554 7.423114
## ZBTB6 GTF2F2 PPTC7 S100A10 UCKL1 GFPT1 TXNRD1
## C138 5.823454 9.389657 8.758430 12.83638 6.111825 12.29928 9.722320
## C178 5.772612 9.389404 8.935212 12.96163 5.804949 12.02436 9.879940
## C255 5.401136 9.620334 8.265225 12.67518 5.798833 11.89459 9.817652
## C278 5.791521 9.438320 8.628536 13.01438 6.323175 12.03126 9.746180
## C361 5.875448 9.574509 8.556842 13.17541 6.204027 11.97959 9.883161
## C404 5.438938 9.167088 8.674335 12.60912 6.404336 11.76852 9.358782
## TTC37 FOXJ3 SFMBT2 CAPZA2 TRIQK HLA-A PPP1CB
## C138 8.960884 8.097634 6.338861 9.772705 7.551118 14.35820 10.65243
## C178 8.787633 7.886207 5.963019 9.744489 7.627387 14.91458 10.30639
## C255 8.467340 7.947274 6.151081 9.316179 7.143007 14.52226 10.26970
## C278 8.859144 8.276103 5.691381 9.741212 7.865170 14.63558 10.61591
## C361 8.900995 8.456332 5.987132 9.840701 7.741325 14.32406 10.64574
## C404 8.968724 8.109983 6.084887 9.474755 7.668922 14.46449 10.13952
## IFNG-AS1 KIAA1147 INAFM2 GTF2H5
## C138 4.231069 8.484093 6.502504 9.075439
## C178 3.588871 8.121165 5.932903 8.838176
## C255 4.174709 7.840134 5.937384 8.391291
## C278 3.705884 7.839616 6.452716 9.044693
## C361 3.467413 8.061417 6.569180 9.070075
## C404 3.834260 8.055103 6.038417 8.853218
write.csv(genesbeta.05.lin,
"~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/corr/genesbeta.05.lin.csv",
row.names = T)
################### make clinical as the same pid order of gene #################
## not the same order
## check
sum(as.matrix(rlog.isgs.05.raw) != isgs.05.lin)
## [1] 0
sum(isgs.rld.lin[,234] != clinical[,6])
## [1] 31
sum(isgs.rld.lin$age == clinical$age)
## [1] 3
##
isgs.05.lin.order <- data.frame(isgs.05.lin) %>% dplyr::mutate(pid = row.names(isgs.05.lin))
clinical_order <- base::merge(clinical, isgs.05.lin.order, by = "pid")
clinical_order <- clinical_order[,c(1:18,24)]
write.csv(clinical_order,
"~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/corr/clinical_order.csv",
row.names = F)
## clinical_order$pid == row.names(isgs.05.lin)
########### association ################
## data isgs.05.lin genesbeta.05.lin and clinical
########################## linear regression ##############################
## equal length of outcomes and covariates
gene_IFNReg <- function(gene_matrix, clinical_variable, clin_var_name){
# get names ready
genelistname = base::colnames(gene_matrix)
## number of gene to test, also the number of multiple test
n_gene = ncol(gene_matrix)
## outcome lm
outcome_lm = lapply(1:n_gene, function(i){
lm = lm(gene_matrix[,i]~ clinical_variable + clinical_order$age + clinical_order$sex )
coef = summary(lm)$coefficients[2, ]
return(coef)
})
outcome_lm = data.frame(matrix(unlist(outcome_lm), ncol = 4, byrow = TRUE,
dimnames = list(
c(colnames(gene_matrix)),
c("Estimate", "Std.Error", "t.statistic", "p.value"))))
# adjusted p-value
outcome_lm = outcome_lm %>%
dplyr::mutate(FDR = p.adjust(p.value, "BH", n_gene ),
names = colnames(gene_matrix)) %>%
dplyr::mutate(Estimate = round(Estimate, 10),
Std.Error = round(Std.Error, 10),
t.statistic = round(t.statistic,4)
)%>%
select(names, everything())
# sort by p.value
outcome_lm = outcome_lm[order(outcome_lm$p.value), ]
## sample size
size = sum(!is.na(clinical_variable))
## summary table
return(list(results = data.frame(outcome_lm), size = size, clinical = clin_var_name ))
}
clinical_names <- c("Blood CD4 T Cell Counts (cells/ul)", "Plasma Viral Load", "Tissue HIV RNA (per CD4 T cell)",
"Tissue CD4 T Cell Counts (number/g)", "IL-6 (pg/ml)", "CRP (ug/ml)", "iFABP (pg/ml)",
"sCD27 (U/ml)", "CD14 (ng/ml)", "LPS (pg/ml)", "LTA (OD)",
base::paste("IFN", '\u03b1', sep = "" ), base::paste("IFN", '\u03b2', sep = "" ))
n_clinical <- length(clinical_names)
n_clinical
## [1] 13
clinical_sum <- matrix(NA, 13,8)
for(i in 1:n_clinical) {
## number of clinical virable
j = c(6:18)[i]
cliname = base::colnames(clinical_order)[j]
## linear regression
lin_res_isgs = gene_IFNReg(isgs.05.lin, clinical_order[,j], clinical_names[i])
lin_res_genesbeta = gene_IFNReg(genesbeta.05.lin, clinical_order[,j], clinical_names[i])
## save data
write.xlsx(lin_res_isgs$results,
paste("~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/isgs_", cliname,".xlsx", sep = ""),
sheetName= paste("ISGs_", cliname, sep = "") )
write.xlsx(lin_res_genesbeta$results,
paste("~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/ifnbeta_", cliname,".xlsx", sep = ""),
sheetName= paste("ifnbeta_", cliname, sep = ""))
## check basic
if(lin_res_isgs$size == lin_res_genesbeta$size){
print("Good")
}else stop("sample size wrong")
if(lin_res_isgs$clinical == lin_res_genesbeta$clinical){
print("Good")
}else stop("clinical parameter wrong")
## number of genes
nisgs = nrow(lin_res_isgs$results)
ngenesbeta = nrow(lin_res_genesbeta$results)
################## summary table ###################
### sig prop
isgs.sig.no = sum(lin_res_isgs$results$FDR <= 0.05)
genesbeta.sig.no = sum(lin_res_genesbeta$results$FDR <= 0.05)
if( (isgs.sig.no >= 5) & (genesbeta.sig.no >= 5) ){
prop.test.sig = prop.test(x = c(isgs.sig.no, genesbeta.sig.no), n = c(nisgs, ngenesbeta), correct = FALSE)
sig.p = prop.test.sig$p.value
}else{
prop.test.sig = prop.test(x = c(isgs.sig.no, genesbeta.sig.no), n = c(nisgs, ngenesbeta), correct = TRUE)
sig.p = prop.test.sig$p.value
}
########### volcano plots ################
if(min(lin_res_isgs$results$FDR) <= 0.05){
rownames(lin_res_isgs$results) <- lin_res_isgs$results$names
p1 <- EnhancedVolcano(lin_res_isgs$results ,
lab = rownames(lin_res_isgs$results),
x = "Estimate",
y = "p.value",
pCutoff = ifelse( min(lin_res_isgs$results$FDR) <= 0.05,
lin_res_isgs$results$p.value[max(which(lin_res_isgs$results$FDR <= 0.05))] + 0.005,
0.05),
FCcutoff = round(max(abs(quantile(lin_res_isgs$results$Estimate, c(0.25, 0.75) ))),1),
title = paste("Core ISGs: association with ", lin_res_genesbeta$clinical , sep = ""),
xlim = range(lin_res_isgs$results$Estimate)*1.3,
ylim = c(0, -log10(min(lin_res_isgs$results$p.value)/5000)),
legend=c("NS","Slope","FDR Significant",
"FDR Significant & Slope"),
## select labels to show
# selectLab = c("cg18587484","cg00803922", " cg19425295"),
## point and label size
transcriptPointSize = 2,
transcriptLabSize = 3,
xlab = bquote(~Log[2]~ "Slope"),
ylab = bquote(~-Log[10]~italic(P)),
#Modify border and remove gridlines
gridlines.major = FALSE,
gridlines.minor = FALSE,
border = "full",
borderWidth = 1.0,
borderColour = "black",
# the transparence of the dots
colAlpha = 0.8,
# adjust the legend
legendPosition = "bottom",
legendLabSize = 9,
legendIconSize = 3,
# connectors
DrawConnectors = TRUE,
#
widthConnectors = 0.2,
#
colConnectors = "grey40",
col = c("grey30", "forestgreen", "royalblue", "tomato")
)
ggsave(paste("Volcanol_Plot_ISGs_", cliname, sep = ""), width = 6, height = 9, device = "tiff", path = "~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/Reports/plots", dpi = 300)
} else{print("No Sig.")}
if(min(lin_res_genesbeta$results$FDR) <= 0.05){
rownames(lin_res_genesbeta$results) <- lin_res_genesbeta$results$names
p1 <- EnhancedVolcano(lin_res_genesbeta$results ,
lab = rownames(lin_res_genesbeta$results),
x = "Estimate",
y = "p.value",
pCutoff = ifelse( min(lin_res_genesbeta$results$FDR) <= 0.05,
lin_res_genesbeta$results$p.value[max(which(lin_res_genesbeta$results$FDR <= 0.05))] + 0.005,
0.005),
FCcutoff = max(abs(quantile(lin_res_genesbeta$results$Estimate, c(0.25, 0.75) ))) ,
title = paste("IFNBeta Genes: association with ", lin_res_genesbeta$clinical , sep = ""),
xlim = range(lin_res_genesbeta$results$Estimate)*1.3,
ylim = c(0, -log10(min(lin_res_genesbeta$results$p.value)/5000)),
legend=c("NS","Slope","FDR Significant",
"FDR Significant & Slope"),
## select labels to show
# selectLab = c("cg18587484","cg00803922", " cg19425295"),
## point and label size
transcriptPointSize = 2,
transcriptLabSize = 3,
xlab = bquote("Slope"),
ylab = bquote(~-Log[10]~italic(P)),
#Modify border and remove gridlines
gridlines.major = FALSE,
gridlines.minor = FALSE,
border = "full",
borderWidth = 1.0,
borderColour = "black",
# the transparence of the dots
colAlpha = 0.8,
# adjust the legend
legendPosition = "bottom",
legendLabSize = 9,
legendIconSize = 3,
# connectors
DrawConnectors = TRUE,
#
widthConnectors = 0.2,
#
colConnectors = "grey40",
col = c("grey30", "forestgreen", "royalblue", "tomato")
)
ggsave(paste("Volcanol_Plot_IFNBeta_", cliname, sep = ""), width = 6, height = 9, device = "tiff", path = "~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/Reports/plots", dpi = 300)
} else{print("No Sig.")}
## positive prop
isgs.pos.no = sum(lin_res_isgs$results$Estimate > 0)
genesbeta.pos.no = sum(lin_res_genesbeta$results$Estimate > 0)
if( (isgs.pos.no >= 5) & (genesbeta.pos.no >= 5) ){
prop.test.pos = prop.test(x = c(isgs.pos.no, genesbeta.pos.no), n = c(nisgs, ngenesbeta), correct = FALSE)
pos.p = prop.test.pos$p.value
}else{
prop.test.pos = prop.test(x = c(isgs.pos.no, genesbeta.pos.no), n = c(nisgs, ngenesbeta), correct = TRUE)
pos.p = prop.test.pos$p.value
}
## If you check prop.test, chisq.test and z-test on your data then they all give you the same p-value
## continuity correction if anyone less than 5
## the clinical summary table
clinical_sum[i, ] <- c(lin_res_genesbeta$clinical, lin_res_genesbeta$size,
isgs.sig.no/nisgs, genesbeta.sig.no/ngenesbeta , sig.p,
isgs.pos.no/nisgs,
genesbeta.pos.no/ngenesbeta , pos.p)
colnames(clinical_sum) <- c("Clinical Parameter", "Sample Size", "ISGs: Sig. Prop.",
"IFNbeta Genes: Sig.", "p value",
"ISGs: Positive Corr. Prop.",
"IFNbeta Genes: Pos.", "p value (Pos)")
}
## [1] "Good"
## [1] "Good"
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## [1] "No Sig."
## [1] "Good"
## [1] "Good"
## clinical_sum
write.xlsx(clinical_sum, "~/Documents/gitlab/Cario_RNASeq_Microbiom_Inte/DataProcessed/clinical_summary.xlsx")
clinical_sum[,c(3,4,6,7)] <- round(as.numeric( as.character( clinical_sum[,c(3,4,6,7) ]) ), 4)
clinical_sum[,c(5,8)] <- format(as.numeric( as.character( clinical_sum[,c(5,8) ]) ), digits = 3, scientific = TRUE)
clinical_sum[12:13,1] <- c("IFNalpha", "IFNbeta")
kable(data.frame(clinical_sum[,c(1:5)]), digits = c(2,2,4,4,40))
| Blood CD4 T Cell Counts (cells/ul) |
32 |
0.3419 |
0.8846 |
1.26e-18 |
| Plasma Viral Load |
19 |
0 |
0 |
NaN |
| Tissue HIV RNA (per CD4 T cell) |
19 |
0 |
0 |
NaN |
| Tissue CD4 T Cell Counts (number/g) |
32 |
0 |
0 |
NaN |
| IL-6 (pg/ml) |
32 |
0 |
0.5615 |
1.77e-21 |
| CRP (ug/ml) |
32 |
0 |
0 |
NaN |
| iFABP (pg/ml) |
32 |
0 |
0 |
NaN |
| sCD27 (U/ml) |
32 |
0 |
0 |
NaN |
| CD14 (ng/ml) |
30 |
0 |
0 |
NaN |
| LPS (pg/ml) |
30 |
0.8803 |
0.9308 |
1.73e-01 |
| LTA (OD) |
30 |
0 |
0 |
NaN |
| IFNalpha |
29 |
0.0085 |
0 |
9.58e-01 |
| IFNbeta |
29 |
0.9145 |
0.9692 |
6.34e-02 |
kable(data.frame(clinical_sum[,c(1,2,6:8)]), digits = c(2,2,4,4,40))
| Blood CD4 T Cell Counts (cells/ul) |
32 |
0.1197 |
0.9308 |
1.98e-37 |
| Plasma Viral Load |
19 |
0.4017 |
0.9538 |
6.14e-21 |
| Tissue HIV RNA (per CD4 T cell) |
19 |
0.7009 |
0.6385 |
2.98e-01 |
| Tissue CD4 T Cell Counts (number/g) |
32 |
0.3419 |
0.9231 |
1.32e-21 |
| IL-6 (pg/ml) |
32 |
0.8889 |
0.0692 |
3.91e-38 |
| CRP (ug/ml) |
32 |
0.8291 |
0.0923 |
2.48e-31 |
| iFABP (pg/ml) |
32 |
0.4701 |
0.2231 |
4.28e-05 |
| sCD27 (U/ml) |
32 |
0.8803 |
0.0769 |
1.05e-36 |
| CD14 (ng/ml) |
30 |
0.8718 |
0.0692 |
9.75e-37 |
| LPS (pg/ml) |
30 |
0.8803 |
0.0692 |
1.98e-37 |
| LTA (OD) |
30 |
0.8803 |
0.0692 |
1.98e-37 |
| IFNalpha |
29 |
0.1197 |
0.9308 |
1.98e-37 |
| IFNbeta |
29 |
0.8803 |
0.0692 |
1.98e-37 |